Archaea and the Prokaryote-to-Eukaryote Transition - Europe

47 Pages·1997·0.94 MB·English

MICROBIOLOGYANDMOLECULARBIOLOGYREVIEWS,Dec.1997,p.456–502 Vol.61,No.4
1092-2172/97/$04.0010
Copyright©1997,AmericanSocietyforMicrobiology
Archaea and the Prokaryote-to-Eukaryote Transition
JAMESR.BROWN1,2*ANDW.FORDDOOLITTLE1
CanadianInstituteforAdvancedResearch,DepartmentofBiochemistry,DalhousieUniversity,Halifax,
NovaScotia,Canada,1andDepartmentofBioinformatics,SmithKlineBeecham
Pharmaceuticals,Collegeville,Pennsylvania2
INTRODUCTION.......................................................................................................................................................457
ARCHAEAALONE.....................................................................................................................................................457
ARCHAEAANDBACTERIA......................................................................................................................................458
ARCHAEAANDEUKARYOTES..............................................................................................................................459
ROOTINGTHEUNIVERSALTREE......................................................................................................................460
ACCEPTANCEANDDOUBT...................................................................................................................................461
ORIGINOFEUKARYOTES....................................................................................................................................462
UNIVERSALPROTEINGENETREES..................................................................................................................465
MethodsandCaveats.............................................................................................................................................465
Sequences.............................................................................................................................................................465
Phylogeneticmethods.........................................................................................................................................465
Interdomaindistanceestimates........................................................................................................................466
DNAReplicationandRepairEnzymes................................................................................................................466
DNAgyrasesandtopoisomerases.....................................................................................................................466
DNApolymeraseB..............................................................................................................................................467
Photolyase............................................................................................................................................................468
TranscriptionalProteins........................................................................................................................................468
TranslationalProteins...........................................................................................................................................469
Elongationfactors...............................................................................................................................................470
Aminoacyl-tRNAsynthetases.............................................................................................................................470
Ribosomalproteins.............................................................................................................................................473
EnzymesinCentralMetabolism...........................................................................................................................473
Glyceraldehyde3-phosphatedehydrogenase...................................................................................................478
3-Phosphoglyceratekinase.................................................................................................................................479
Enolase.................................................................................................................................................................479
Acetyl-CoAsynthetase........................................................................................................................................479
Citratesynthase..................................................................................................................................................479
Malatedehydrogenase........................................................................................................................................481
AminoAcidBiosynthesisandDegradation.........................................................................................................481
Aminotransferases..............................................................................................................................................481
Glutaminesynthetase.........................................................................................................................................482
Glutamatedehydrogenase..................................................................................................................................483
Argininosuccinatesynthetase............................................................................................................................483
Carbamoylphosphatesynthetase.....................................................................................................................483
Tryptophanbiosynthesis....................................................................................................................................484
Histidinebiosynthesis........................................................................................................................................484
Pyrroline-5-carboxylatereductase....................................................................................................................486
Cofactors..................................................................................................................................................................486
PurineRibonucleotideBiosynthesis.....................................................................................................................486
IMPdehydrogenase............................................................................................................................................486
Phosphoribosylformylglycinamidinesynthetase.............................................................................................486
Respiration...............................................................................................................................................................486
PorphyrinBiosynthesis..........................................................................................................................................490
Glutamyl-tRNAreductase..................................................................................................................................490
5-Aminolevulinicaciddehydratase...................................................................................................................490
Chaperonins.............................................................................................................................................................490
Membranes..............................................................................................................................................................490
EVOLUTIONARYTRENDSINMULTIPLEPROTEINPHYLOGENIES........................................................491
NearestDomains.....................................................................................................................................................491
IntegrityofDomains..............................................................................................................................................491
*Correspondingauthor.Mailingaddress:DepartmentofBioinfor-
matics, SmithKline Beecham Pharmaceuticals, P.O. Box 5089,
UP1345, Collegeville, PA 19426-0989. Phone: [phone]. Fax:
[phone].E-mail:[email protected].
456
VOL.61,1997 ARCHAEA AND THE PROKARYOTE-TO-EUKARYOTE TRANSITION 457
Endosymbiosis—MoreThanJustOrganelles.....................................................................................................493
RatesAin’tMisbehavin’.........................................................................................................................................493
WHATNEXT?.............................................................................................................................................................494
ACKNOWLEDGMENTS...........................................................................................................................................495
REFERENCES............................................................................................................................................................495
INTRODUCTION theupheaval,ofmacroevolutionarytheory(336).Thus,asec-
ond goal of this review is to attempt a synthesis of universal
Forover50years,scientistswereconfidentwiththenotion treesbasedondifferentproteincodinggenesbyreviewingand
thatthereweretwobasickindsoflivingorganisms,eubacteria occasionallyupdatingearlierphylogeneticstudiesandbyadd-
andeukaryotes(306–308).Inthelate1970s,thisfundamental ing analyses of new gene families. The dynamic growth of
beliefwasshatteredbytherevelationsofWoeseandcoworkers sequence databases makes it impossible to assemble a highly
that life consisted not of two but three distinct groups of currentyetcomprehensivecollectionofspeciesorgenesprior
organisms (123, 337)—eukaryotes and two kinds of pro- to publication. Therefore, the multiple gene phylogenies pre-
karyotes, the eubacteria and the archaebacteria. Since then, sentedherearebestseenasageneraloverviewoftheuniversal
our knowledge of the latter has reached the point where the treeoflifefromdifferentbiochemicalperspectives.
firstcompletegenomesequencefromanarchaebacterium(49)
isnowknown,withseveralmoresoontofollow(31,58,161a). ARCHAEAALONE
GiventhegrowthofDNAsequencedatabases,scienceisnow
poised to make broad and sweeping comparisons of living In1990,Woeseetal.(339)stronglyadvocatedthereplace-
organisms.However,wellbeforethedawningofthisnewage mentofthebipartateviewoflifewithanewtripartitescheme
of entire genome sequences, the cumulative efforts of many based on three urkingdoms or domains; the Bacteria (eubac-
highly determined and capable researchers had led to an im- teria), Archaea (archaebacteria) and Eucarya (eukaryotes)
pressiveknowledgebaseaboutthearchaebacteria.Thisreview (Fig.1).Therationalebehindthisrevisioncamefromagrow-
isamodestattempttosummarizesomeofthatresearchinthe ingbodyofevidence,inparticularrRNAphylogenies,thatthe
context of what has been learned about the nature of the archaebacteria were worthy of the same taxonomic status as
universaltreeoflivingorganisms.Hopefully,fromviewingthe eukaryotes and eubacteria. Since then, the database of small-
archaebacteriainthisway,abetterappreciationcanbegained subunitrRNAsequenceshasgrowntoincludeover2,000pro-
abouttheevolutionarysignificanceoftheseremarkableorgan- karyotesandseveralhundredeukaryotes.Despitetheaddition
isms. ofalargenumberofnewspecies,theexistenceofthreemajor
Contemporary views on early cellular evolution have been groupsorcladesoforganismsisconsistentthroughoutrRNA
stronglyshapedbymolecularphylogenetics.EversinceWoese phylogenies(59,246,247,303,336).
andcoworkersdemonstratedthedistinctivenessofarchaebac- However, the three-domain classification has been con-
teria on the basis of cluster dendrograms of data based on tested, most notably by Mayr (232), Margulis and Guerrero
RNase T oligonucleotide catalogs of rRNAs, phylogenetic (224), and Cavalier-Smith (57). As a result, there is an awk-
1
analyseshaveplayedapivotalroleinthematuration,andoften wardcoexistencebetweentheterminologyoftheoldandnew
FIG. 1. SchematicdrawingofauniversalrRNAtreeshowingtherelativepositionsofevolutionarypivotalgroupsinthedomainsBacteria,Archaea,andEucarya.
Thelocationoftheroot(thecenancestor)correspondstothatproposedbyreciprocallyrootedgenephylogenies(43,133,164).ThequestionmarkbesidetheArchezoa
groupMicrosporidiadenotesrecentsuggestionsthatitmightbranchhigherintheeukaryoticportionofthetree.(Branchlengthshavenomeaninginthistree.)
458 BROWN AND DOOLITTLE MICROBIOL.MOL.BIOL.REV.
schemesintheliterature.Sincethetripartateschemebasically but ADP-linked in Pyrococcus (182). The conversion of pyru-
suggests new subdivisions only in the prokaryotes, here we vate to acetate, a reaction which bridges glycolytic and citric
refer to the former archaebacteria and eubacteria as the ar- acidcycles,iscatalyzedbyapyruvatedehydrogenasemultien-
chaeaandbacteria,whileeukaryoteswillstillbecalledassuch. zyme complex in bacteria and eukaryotes, whereas archaea
According to rRNA trees, there are two groups within the and some anaerobic eukaryotes (Entamoeba, Giardia, and
Archaea: the kingdoms Crenarchaeota and Euryarchaeota Trichomonas) appear to employ pyruvate:ferredoxin oxi-
(336).ThekingdomCrenarchaeotagenerallyconsistsofhyper- doreductase (81, 294). Dihydrolipoamide dehydrogenase, a
thermophiles or thermoacidophiles (some genera are Sulfolo- componentofthepyruvatedehydrogenasecomplex,hasbeen
bus,Desulfurococcus,Pyrodictium,ThermoproteusandThermo- detectedinhalophilicarchaea,althoughitsfunctionisunclear
filum).ThekingdomEuryarchaeotaspansabroaderecological (84).
rangeandincludeshyperthermophiles(somegeneraarePyro-
coccus and Thermococcus), methanogens (e.g., Methanosar-
ARCHAEAANDBACTERIA
cina), halophiles (some genera are Halobacterium and
Haloferax),andeventhermophilicmethanogens(somegenera ThemembersoftheArchaeaandBacteriaareunitedinthe
areMethanothermus,Methanobacterium,andMethanococcus). “realmofprokaryotes”bysimilargeneralcellsizes,thelackof
Recent PCR amplifications of rRNA sequences from water a nuclear membrane and organelles, and the presence of a
and sediment samples have revealed a plethora of new ar- large circular chromosome occasionally accompanied by one
chaealspeciesbelongingtoeitherkingdomlivinginmesophilic or more smaller circular DNA plasmids. As an example, the
environments such as temperate marine coastal waters, the chromosomecomplementofthehalophilicarchaeonHaloferax
Antarctic Ocean, freshwater lakes, and even marine sponges volcanii consists of one large circular genome roughly 2.92
(87, 88, 125, 261, 310). Recently, PCR surveys of hot spring Mbp in size and four smaller plasmid genomes with sizes of
microbiota detected new archaeal rRNA sequences that 690,442,86,and6kbp(62).Nearlyallofthe60to70identified
brancheitherdeeplywithintheCrenarchaeotaorjustbelowthe H.volcaniigenesmaptothelargecirculargenome.Although
Crenarchaeota-Euryarchaeota divergence (14, 15). As such, the origin of DNA replication of any archaeal large chromo-
these “organisms” have been tentatively assigned to a third somehasyettobeconfirmedexperimentally,atpresent,there
kingdom,theKorarchaeota(Fig.1). is little suggestion for any significant departure from the bac-
It is also important to consider cellular and biochemical terial model of a single replication initiation site (122). The
features of archaea with respect to the coherence of the do- overall closer similarity between archaeal and bacterial topo-
mainArchaeaitselfanditsevolutionaryrelationshiptoBacte- isomerases and gyrases provides indirect evidence of compa-
ria and eukaryotes. The comparative biochemistry and the rablechromosomestructureamongthetwogroups.
cellularbiologyofArchaea,Bacteria,andeukaryoteshavebeen Many archaeal genes appear to be organized into Bacteria-
extensively reviewed elsewhere; thus, only the salient points like operons. Furthermore, many archaeal operons and gene
willbediscussedhere(47,175,181,342).Archaeahavesome clustersarearrangedinasimilarfashiontothoseoftheBac-
uniquecharacteristicsaswellasuniquecombinationsofchar- teria (reviewed in references 181 and 268). As an example,
acteristicsoncethoughttobeexclusivetoeitherthebacteriaor ribosomaloperonsinbacteriaandchloroplastsarearrangedin
eukaryotes. Some solely archaeal characteristics include iso- theorder16S-23S-5S.Archaeahavethesameorganizationfor
pranyl ether lipids, the absence of acyl ester lipids and fatty these rRNAs with some variation, such as a tRNAAla gene
acidsynthetase,modifiedtRNAmolecules,asplitinoneofthe inserted between the 16S and 23S genes of methanogens and
RNA polymerase subunits, and a specific range of antibiotic halophilesandadistallocationofthe5SrRNAgeneinsome
sensitivities(reviewedinreferences175,181,and187). thermoacidophiles and methanogens (reviewed in reference
The structure of archaeal membranes has been thoroughly 47).
reviewed elsewhere (127, 174, 194). Briefly, archaeal lipids In Escherichia coli, the ribosomal proteins RP L11 and RP
differfromthoseofbacteriaandeukaryotesinfoursignificant L1 are clustered upstream of another group, containing RP
ways. First, Archaea have ether linkages established between L10 and RP L12. These genes occur in the same order in
glycerolandhydrocarbonchainswhilebacteriaandeukaryotes Sulfolobus solfataricus and Halobacterium cutirubrum, while
have ester linkages. Second, archaea have highly methyl- Methanococcus vannielii has RP L11 translocated (12, 269,
branchedisopranylchains,whilehydrocarbonsinbacteriaand 296).Ofthe11genesintheE.colispectinomycin(spc)operon,
eukaryotes are predominantly straight-chain fatty acyl chains. thesameorderoccursfor9and11genesinS.acidocaldarius
Third, archaeal glycerol ethers contain 2,3-sn-glycerol, which and Methanococcus vannielii, respectively (8, 268). Both spe-
differs from the 1,2-sn-glycerols found in the two other do- cies have three small additional open reading frames (ORFs)
mains.Fourth,somelipidsinarchaeaaretetraethersforwhich withintheirspcoperons.
ester lipids have no comparable structures (127). Some lipid Incomparisontotheeight-geneS10operoninE.coli,those
biosyntheticenzymesinarchaeaarealsodifferent.Themeth- ofMethanococcusvannieliiandHalobacteriummarismortuiare
anogen Methanobacterium thermoautotrophicum has a bifunc- missingthefirstgene,RPS10,buthavetheremainingsevenin
tional prenyltransferase that provides precursors to both similarorders(7).InE.coli,theS10operonisdistallylocated
squalene and isoprenoid glyceryl lipids, whereas bacteria and from the streptomycin (str) operon. The str operon has been
eukaryotes use separate enzymes for the synthesis of these sequencedfromawidephylogeneticrangeofbacteria,andin
short-chainmolecules(64,65). mostcases,thegenesforRPS12,RPS7,elongationfactorG
AmongspeciesofArchaea,thereareavarietyofmetabolic (EF-G) (fus), and EF-Tu (tuf) are found. However, the str
regimeswhichdiffergreatlyfromthebetter-knownmetabolic operonofthehyperthermophilicbacteriumAquifexpyrophilus,
pathways of the Bacteria and eukaryotes (reviewed in refer- whichisthedeepest-branchingbacterialspeciesinrRNAtrees
ences81through83and294).Forexample,bothATP-depen- (50),lacksbothribosomalproteingenes(31).Othervariations
dentandpyrophosphate-dependentphosphofructokinasescan includethetranslocationofthegeneforRPS10fromtheS10
occur in bacteria and eukaryotes, while archaea use either operon to downstream of tuf in the cyanobacterial Spirulina
ADP-dependentorpyrophosphate-linkedkinases.Hexokinase platenis(287)andCyanophoraparadoxacyanelles(242).
isATPdependentinbacteria,eukaryotes,andThermoproteus In the archaeon M. vannielii, the str operon is similarly or-
VOL.61,1997 ARCHAEA AND THE PROKARYOTE-TO-EUKARYOTE TRANSITION 459
ganized,withtheRPS10genedownstreamoftheEf-1agene Archaealandbacterialprotein-codinggeneslackspliceoso-
(bacterialEF-GandEF-TuarehomologoustoEF-2andEF- mal introns typically found in eukaryotic genes. A full discus-
1a, respectively, from archaea and eukaryotes). The gene or- sion of the origin and distribution of introns is beyond the
der is varied in S. acidocaldarius, where the EF-2 gene is scope of this review. Noteworthy is that when comparing ho-
missingandatRNASergenefollowsRPS10(10).InPyrococ- mologous genes, introns found in “higher eukaryotes,” the
cus furiosus, the genes for Ef-1a, RP S10, and tRNASer are metazoans, are frequently absent in “lower eukaryotes,” i.e.,
together but RP S7 is absent (76), while in H. halobium, RP the protists (250). Therefore, the absence of spliceosomal in-
S12,RPS7,andEF-2arepresentbutEF-1aandRPS10are trons should not be considered a defining characteristic of
absent(163,214). prokaryotes. The genes encoding 16S and 23S rRNAs and
The operons encoding the three largest subunits of DNA- tRNAsinseveralarchaeahaveintronswithORFsthatcorre-
dependentRNApolymerase(RNAP)intheArchaeaandBac- spondtothehomingendonucleasesofgroupIintronsfoundin
teria can be potentially traced back to an ancestral organiza- mitochondriaandbacteriophages(22,47).Inteinsareunusual
tion.Here,thetranscriptionalpolarityandgeneorderoftheS. introns spliced at the protein rather than the mRNA level,
acidocaldarius RNAP (rpo) subunits B, A1, and A2 are re- which were first found in the catalytic subunit of the yeast
versedincomparisontoE.coli(177).Furthermore,theE.coli vacuolartypeATPase(158,172).Thefirstarchaealinteinwas
genes nusA, encoding a transcription termination factor, and found in the DNA polymerase gene of Thermococcus litoralis
infB, encoding translation initiation factor 2, are located up- (254).Severalnewinteininsertionswerereportedinthewhole
streamoftherpooperoninthesametranscriptionalpolarity. genomesequenceofM.jannaschii(49).
In Sulfolobus, the rpo operon splits the nusA-infB operon in
two. The infB gene is now located downstream of the rpo
operon, with the opposite transcription polarity, while the ARCHAEAANDEUKARYOTES
nusAgeneissituatedupstreambetweentworibosomalprotein
genesandisprobablytranscribedinthesamedirection.Keel- Although the domains Archaea and Bacteria appear very
ingetal.(177)suggestedthatasingleinversioneventmightbe similar in terms of general genome organization, many ar-
sufficienttoexplainthismajorrearrangementbetweenE.coli chaeal genes show greater similarity to eukaryotic homologs.
andSulfolobusrpooperons. HintsofgenetichomologyamongtheArchaeaandeukaryotes
LikemRNAsintheBacteria,archaealmRNAsdonothave were found in early studies with antibiotics (summarized in
59-endcapsandoftenhaveShine-Dalgarnoribosomebinding reference 5). Bacteria are sensitive to streptomycin, an anti-
sites (reviewed in reference 5). However, the locations of pu- 70S ribosome-directed inhibitor. Archaea and eukaryotes are
tative Shine-Dalgarno sequences relative to the translational both refractory to streptomycin but are sensitive to certain
initiation codon are more variable in the members of the Ar- anti-80S ribosome directed inhibitors (such as anisomycin).
chaea,andtheupstreamsequencesofseveralhighlyexpressed Archaea and eukaryotes also share sensitivity to aphidicolin,
genes bear little resemblance to Shine-Dalgarno motifs (see aninhibitorofDNApolymerase,towhichbacteriaarerefrac-
Fig. 6 in reference 268). Little is known about the actual tory(reviewedinreference122).
process of translation initiation in the Archaea, although sev- Later studies showed significant similarities between ar-
eral sequences similar to eukaryotic translation initiation fac- chaeal and eukaryotic DNA replication, transcriptional, and
torshavebeendetectedin Sulfolobus(17,178)and Methano- translationalcomponents.ArchaealandeukaryoticDNApoly-
coccus jannaschii (49). However, even in the Bacteria and merasesarehomologousandnotrelatedtoanybacterialDNA
eukaryotes,theevolutionaryrelationshipsandexactfunctions polymerase except that of E. coli (reviewed in reference 99).
ofseveralinitiationfactorsareunclear.Untilproteinsynthesis Several other DNA replication components are similarly
has been better studied, one can only predict that translation shared only between Archaea and eukaryotes. Archaeal
initiationintheArchaeaprobablydeviatessomehowfromthe RNAPs are evolutionarily closer to those of eukaryotes (263,
E.colimodel. 345). In addition, bacterial RNAPs have a simpler structure
ThebacterialcelldivisionproteinFtsZhasbeendiscovered composed of only four major subunits while eukaryotic and
inseveralspeciesofArchaea(19,327).FtsZisthoughttobea archaealRNAPshaveaminimumofsevensubunits,ofwhich
distanthomologtoeukaryotictubulins,sincebothproteinsare several are homologous (139, 207, 345). Phylogenetic trees
GTPases that polymerize into filaments in the presence of obtainedwiththesequencesforlargeRNAPsubunitsstrongly
GTP(107).Arabidopsishasanucleus-encodedFtsZhomolog show that eukaryotic and archaeal genes are close relatives
whichisdirectedtothechloroplast(248).Phylogeneticanalysis (188,263,344).TheArchaeaandeukaryotesalsoshareother
also supports the notion that FtsZ is a distant homolog of featuresoftranscriptionthatareapparentlyabsentintheBac-
tubulin, with the FtsZ of the Archaea and Bacteria forming teria.TheseincludeTATAbox-likebindingsites(275,345)and
distinctyetcloselyrelatedgroups(19).Amongtheseprokary- sometranscriptionfactors(226,249,273,283).
oticFtsZhomologs,thoseoftheArchaeaaremarginallycloser Pre-rRNAprocessingineukaryotesinvolvesmanydifferent
to the large eukaryotic family of tubulins. Some cell division small nucleolar rRNAs (snoRNAs) associating with the pro-
proteinshavebeenidentifiedintheM.jannaschiigenomebut tein fibrillarin. The gene for fibrillarin has been cloned and
nottheentiresuiteofgenesknowntofunctionincellseptation sequenced from methanogenic members of the Archaea (6,
orchromosomepartitioningintheBacteria(49).Eithermore 49), and antibodies against fibrillarin have precipitated sno
celldivisionhomologsremaintobefound,orthearchaeause RNAs in Sulfolobus (91). Although a report of U3-like RNA
auniquesystembasedonparticularBacteria-likecomponents. cloned from Sulfolobus acidocaldarius (258) was subsequently
ManymembersoftheArchaeaalsohavetypeIIrestriction determinedtobeanerror(284),itisstillpossiblethatrelated
enzymesystems,similartothoseoftheBacteria(summarized snoRNAsareinvolvedintheprocessingofarchaealpre-rRNA
in reference 47). Plasmid genes encoding for restriction- (96).IntronsintRNAgenesoftheArchaeaandeukaryotesare
modification enzymes, endodeoxyribonuclease and DNA meth- ofsimilarsizeandoccurinmostlythesamepositions,although
yltransferase,inMethanobacteriumthermoformiciumshowsig- some archaeal tRNA introns have shifted locations (24). The
nificant homology to those of the bacterium Neisseria gonor- excisionoftRNAintronsineukaryotesinvolvesasite-specific
rhoeae(244). endonuclease which is composed of two subunits (186, 321).
460 BROWN AND DOOLITTLE MICROBIOL.MOL.BIOL.REV.
Thesubunitsaresimilartoeachotheraswellasbeinghomol- proteins, known as HU, which are not evolutionary linked to
ogoustoarchaealtRNAendonucleases. histones,althoughtheyperformsimilarfunctions(30).
MembersoftheArchaeaandeukaryotesshareapathwayof In summary, there are some features that distinguish the
isoprenoid biosynthesis that involves the synthesis of meval- Archaea from the Bacteria and eukaryotes, most notably the
onate from 3-hydroxy-3-methylglutaryl coenzyme A (HMG- structureandcompositionoftheirmembranes.Primarily,the
CoA) by the enzyme HMGCoA reductase. The first archaeal membersoftheArchaeaareuniqueinhavingacombinationof
HMGCoA reductase gene was sequenced from H. volcanii traitswhich,untilnow,werebelievedtobeexclusivetoeither
(204). The gene and the enzyme activity have been recently the Bacteria or eukaryotes. However, until we have genome
characterized from S. solfataricus (32). Bacteria lack HMG- sequences from more diverse groups of prokaryotes and eu-
CoA,although Pseudomonasmevaloniihasahighlydivergent karyotes, evolutionary scenarios based on the presence of a
HMGCoAreductase,whichmightbeaspecificadaptationto characterintwodomainsanditspresumedabsenceinthethird
theuseofmevalonateasacarbonsource(129). mustbeconsideredtobehighlyprovisional.
In the Bacteria, including the deep-branching thermophile
Thermotoga maritima, acetyl-CoA is converted to acetate
throughthecoordinatedactivitiesoftwoenzymes,phosphate ROOTINGTHEUNIVERSALTREE
acetyltransferase and acetate kinase. However, hyperthermo-
philic archaea employ a single enzyme, an ADP-forming There are three possible scenarios for the evolution of the
acetyl-CoAsynthetasewhichisabsentinbacteria(reviewedin threedomainsoflife:(i)Bacteriadivergedfirstfromalineage
reference 294). Interestingly, ADP-forming acetyl-CoA syn- producingArchaeaandeukaryotes,(ii)aproto-eukaryoticlin-
eagedivergedfromafullyprokaryotic(BacteriaandArchaea)
thetaseswereinitiallydiscoveredintwoanaerobiceukaryotes,
lineage, or (iii) Archaea diverged from a lineage leading to
Entamoeba histolytica (274) and Giardia lamblia (220). How-
eukaryotes and Bacteria. However, on the basis of a solitary
ever,theopposingactivationofacetatebacktoacetyl-CoAin
gene, it is impossible to derive an objective rooting for the
the Archaea is not catalyzed by acetyl-CoA synthetase (ADP-
universal tree. Typically, the rooting for a particular organis-
forming). For this reaction, methanogens use acetate kinase
maltree,forexample,allmammalianspecies,wouldbedeter-
andphosphateacetyltransferase(bothencodinggenesinMeth-
mined by including sequence data from a known outgroup
anosarcina thermophila have been sequenced and are homol-
species,suchassomecold-bloodedvertebrates.However,out-
ogoustothoseofE.coli[211])whileThermoproteusneutrophi-
groupspeciesarenotavailableforagenetreeconsistingofall
lus, a member of the Crenarchaeota, uses an AMP-forming
livingorganismsunlessspecificassumptionsaremadesuchas
acetyl-CoAsynthetase(294).
theprogressionoflifefromaprokaryotictoaeukaryoticcell.
Proteindegradationisanimportantregulatorystepinmany
Therefore,thebranchingorderofthethreedomainsemerging
cellular processes. In eukaryotes, an abundant protein com-
from their last common ancestor—which Fitch and Upper
plex, the 26S proteasome, is responsible for ATP-dependent
calledthecenancestor(116)—canonlybeestablishedbysome
proteolysis.The26Sproteasomeconsistsofa20Scoresubunit
method unrelated to either outgroup organisms or theories
flanked by two 19S caps (222). Archaea have a reduced pro-
aboutprimitiveandadvancedstates.
teasome complex equivalent to the 20S subunit which was
In1989,asolutiontothisproblem,usingancientduplicated
reported first for Thermoplasma acidophilum (80, 265, 348,
genes, was simultaneously proposed in separate papers by
349)andlaterforMethanosarcinathermophila(230),Pyrococ-
Gogarten et al. (133) and Iwabe et al. (164). Their collective
cus furiosus (18), and Methanococcus jannaschii (49). The eu-
reasoning was as follows: although there can be no organism
karyoticproteasomeisacomplexstructureinvolvingatleast34
which is an outgroup for a tree relating all organisms, one
polypeptides,whilethefunctionalT.acidophilumproteasome
could root a tree based on the sequences of outgroup genes
consistsofonlytwosubunits(330,348).Sequencesimilarities
produced by an early gene duplication (Fig. 2A). Iwabe et al.
betweeneukaryoticproteasomalsubunitsandthelarge(a)or
(164) applied this concept by reciprocal rooting of trees for
small (b) subunits of the Thermoplasma proteasome suggest
paralogous elongation factor genes. Elongation factors are a
that the simplified archaeal proteasome might be ancestral
familyofGTP-bindingproteinswhichfacilitatethebindingof
(348, 349). Many bacteria have sequences similar to 20S pro- aminoacylated tRNA molecules to the ribosome (EF-Tu in
teasome b-type subunits, further suggesting that proteasomes BacteriaandEF-1aineukaryotesandArchaea)andthetrans-
orproteasome-likeprecursorsexistedinthelastcommonan- locationofpeptidyl-tRNA(EF-GinBacteriaandEF-2ineu-
cestor (223). However, bacterial multisubunit proteasomes karyotesandArchaea).Iwabeetal.alignedaminoacidsfrom
have been reported only in actinomycetes, and it has been five conserved regions shared by the EF-Tu/1a and EF-G/2
proposedthatthosewerehorizontallytransferredfromeither genes of the archaeon Methanococcus vannielii and several
aeukaryoteoranarchaeon(222). species of the Bacteria and eukaryotes. According to protein
StudiesofarchaealDNA-bindingproteinsorHMf,initially sequencesimilarityandneighbor-joiningtrees,boththeEF-1a
from the methanogen Methanothermus fervidus, suggest a and EF-2 genes of the Archaea were more similar to their
strong similarity to eukaryotic histones both at the primary respectiveeukaryoticratherthanbacterialhomologs.
sequence level (138, 290) and in three-dimensional structure Gogartenetal.(133)developedcompositetreesbasedona
(309). Histone-encoding genes have now been determined secondgeneduplication,thatoftheVtype(foundinArchaea
from different members of the Euryarchaeota, where their and eukaryotes) and F-type (found in Bacteria) ATPase sub-
numbercanvarybetweenspecies(273).Putativearchaealnu- units.ThecatalyticbsubunitofF-typeATPasesismostsimilar
cleosomes differ from eukaryotic nucleosomes in that DNA to the A or 70-kDa subunit of V-type ATPases, while the a
strandsareconstrainedaboutHMfparticlesaspositivesuper- subunitofF-typeATPasesismostsimilartotheBor60-kDa
coils rather than the conventional negative supercoil confor- subunit of V-type ATPases (reviewed in reference 286). In
mation imposed by histones (239, 273). While eukaryotic his- agreement with the elongation factor rooting, reciprocally
tonesformonlyH2A-H2BandH3-H4heterodimers,archaeal rooted ATPase subunits trees showed the archaeon, in this
histonescanassembleasbothhomodimersandheterodimers. caseSulfolobusacidocaldarius,tobeclosertoeukaryotesthan
Archaea also have proteins similar to bacterial DNA-binding totheBacteria.
VOL.61,1997 ARCHAEA AND THE PROKARYOTE-TO-EUKARYOTE TRANSITION 461
more ribosome structures were determined, Lake’s 1988 eo-
cyte tree became untenable. More recently, Rivera and Lake
(278) found new support for the eocyte tree, this time in the
analysis of a specific 11-amino-acid insertion shared in the
EF-1a genes of eukaryotes and the Crenarchaeota but absent
from the Euryarchaeota and Bacteria. This 1992 eocyte tree
resembled the 1988 tree by still having a Crenarchaeota-eu-
karyotecladebutdifferedinthereassignmentofEuryarchaeota
andBacteriaintoindividualclades(Fig.2C).
Cammaranoandcoworkers(53,75,320)addedseveralelon-
gationfactorsequencesfromnewspeciesoftheArchaeaanda
deeplybranchingbacterium(Thermotogamaritima).Although
theydidnotuseareciprocalrooting,theiranalysesofEF-G/2
sequencesshowedstrongsupportforamonophyleticcladeof
theArchaea,subdividedintothekingdomsCrenarchaeotaand
Euryarchaeota. However, another analysis (13) of elongation
factor genes, including many deep-branching species from all
domains,foundsupport,albeitstatisticallyweak,forthediver-
genceofeukaryoteswithintheArchaeaasasistergrouptothe
FIG. 2. Alternativescenariosaboutearlycellularevolution.(A)Conceptual
Crenarchaeota, which somewhat bolsters the eocyte tree of
rootingoftheuniversaltreebyusingparalogousgenes.Supposethatsomegene
(X)wasduplicated(X9andX0)inthecenancestorsuchthatallextantorganisms RiveraandLake(278).
have both genes. Provided that some sequence similarity still exists between Forterreetal.(120)vigorouslyarguedthatneithertheelon-
genes X9 and X0, reciprocally rooted gene trees could be constructed. The
gation factor nor the ATPase data set can settle the issue of
positioningofArchaea(A)andeukaryotes(K)assistergroupswiththeBacteria
(B)astheoutgroup,hasbeenconsistentlysupportedbysuchrootings(43,133, rooting the universal tree. Their major criticisms concerned
164).(B)The1988eocytetreeasproposedbyLakeandcoworkers(199).The thepaucityoftaxa(whichwaslargelyaddressedinthestudyby
Crenarchaeota or eocytes (Eo) form a clade with eukaryotes, while the Eur- Balduafetal.[13])andthefactthatonly120aminoacidscould
tyearricah.a(eCo)taT,hneammeolys,thraelcoepnhtileeosc(yHte)tarnedemadevtohcaantoegdenbsy(RMiv)e,rcaluastnedrLwaitkhethine1B9a9c2- be aligned with confidence between EF-Tu/1a and EF-G/2,
(278).TheeocytesaretheclosestgroupoftheArchaeatotheeukaryotes,with whichare390to460and700to860aminoacidslong,respec-
theEuryarchaeota(A)beingmoredistantlyrelatedalthoughnolongerbranching tively.
withtheBacteria.(D)The“chimeric”or“fusion”hypothesis,whichsuggeststhat
ATPase subunit gene phylogenies are also more problem-
eukaryotesarosewhena“gram-negative”bacteriumengulfedanarchaeonand
componentsoftheirgenomesfused(147,202,342,343). atic. Based on greater similarities between archaeal and eu-
karyotic V-type ATPases over bacterial F F -type ATPases,
0 1
earlier analyses placed the root of the universal tree in the
ACCEPTANCEANDDOUBT Bacteria(133,164).Atthetime,knownbacterialATPaseswere
of the F F type while V-type ATPases were exclusive to the
0 1
Archaebacteriologists (or “archaeologists”) were already Archaeaandeukaryotes.Itwasproposedthatageneduplica-
primed to accept the conclusions of these duplicated gene tion in the cenancestor resulted in the F-type b/V-type A (or
rootings of the universal tree, since early on there was a gen- 70-kDa)subunit,ontheonehand,andtheF-typea/V-typeB
eralfeelingthattheArchaeawassomehowthe“missinglink” (or60-kDa)subunit,ontheother.
betweentheBacteriaandeukaryotes.Atthetime,eukaryote- Subsequently, archaeal V-type ATPases were reported for
likefunctionalandstructuralcharacteristicsofarchaealRNA twobacterialspecies,Thermusthermophilus(322)andEntero-
and DNA polymerases and some ribosomal proteins were coccus hirae (171), and an F -ATPase b-subunit gene was
known.Woeseetal.(339)incorporatedtheproteinrootingin 1
found in the archaeon Methanosarcina barkeri (313) (Fig. 3).
theirformulationofthethreedomains,Archaea,Bacteria,and
Forterre et al. (120) suggested that the ATPase subunit gene
Eucarya.AlthougharchaealandbacterialrRNAsequencesare
family had not been fully determined and that other paralo-
slightlymoresimilar,Woeseetal.placedtherootoftheribo-
gousgenesmightexist.However,HilarioandGogarten(156)
somaltreesuchthatArchaeaandEucaryaweresistergroups.
suggest that the observed distribution of ATPase subunits is
Here, it is important to emphasize that their “archaeal” uni-
the result of a few lateral gene transfers between species of
versaltreewasformulatedfromthreedifferentdataanalyses.
ArchaeaandBacteria.Insupportoftheirview,broadersurveys
The separate monophyly of the Archaea, Bacteria and eu-
havefailedtodetectarchaealV-typeATPasesinotherbacte-
karyotes was suggested by rRNA gene trees (336), while the
rialspecies(132).
grouping of Archaea and eukaryotes together arose from the
More recently, the rooting of the universal tree was at-
reciprocally rooted gene trees for elongation factors and
tempted by using another duplicated gene family, the amino-
ATPasesubunits(133,164).
acyl-tRNAsynthetases(43).Novelisoleucyl-tRNAsynthetases
However, some researchers have seriously challenged the
topologyofthearchaealuniversaltree.InanrRNAtreefirst from species belonging to deep evolutionary lineages of the
proposed in 1988, Lake (199) broke up the Archaea (then Bacteria, Archaea, and eukaryotes were used to construct a
archaebacteria)byplacingtheCrenarchaeota,whichhecalled universalgenetreerootedbyvalyl-andleucyl-tRNAsyntheta-
eocytes,inacladewitheukaryotes,nownamedkaryotes(Fig. ses. The sisterhood of eukaryotes and Archaea, as well as the
2B). Methanogens, halophiles, and members of the Bacteria separate monophyly of all three domains, was strongly sup-
wereinaseparategroupcalledtheparkaryotes,whichnotably portedbythisanalysis.Asimilarconclusionwasreachedinthe
hadtheBacteriainacladewithhalobacteria(200).Thisearly phylogenetic analysis of tryptophanyl- and tyrosyl-tRNA syn-
revisionistuniversaltreewasbasedondifferencesinribosome thetases (46). Now that more archaeal aminoacyl-tRNA syn-
shapes (152, 201) and a novel phylogenetic analysis of rRNA thetasesareknown,furtheropportunitiesexisttoderivemul-
sequences (199). However, as the rRNA data set grew and tiplerooteduniversaltrees.
462 BROWN AND DOOLITTLE MICROBIOL.MOL.BIOL.REV.
FIG. 3. PhylogeniesforATPaseF-typeb/V-typeAsubunit(A)andF-typea/V-typeBsubunit(B)genesfromselectedspecies.Inthisphylogeneticfigureandall
others,thedifferenttypefacesindicatewhetherthespeciesbelongtotheeukaryotes(allcapitals),Archaea(lowercaseboldface),orBacteria(lowercaselightface).
Certainhighlyfamiliarspeciesarereferredtobytheircommongenusorabbreviatedspeciesnamestoconservespace.Eukaryoticgeneswhicharenucleusencoded
yettargetedtothemitochondrion(mito.)orchloroplast(chl.)areindicatedassuch.Genetreeswereconstructedbytheneighbor-joiningmethodbasedonpairwise
distanceestimatesoftheexpectednumberofaminoacidreplacementspersite(0.1inthescalebars).Numbersshowthepercentoccurrenceofnodesin100bootstrap
replications,andonlyvaluesgreaterthan50%areshown.TheprogramsSEQBOOT,PROTDIST,NEIGHBOR,andCONSENSEofthePHYLIP3.57(114)package
wereusedfortheanalysis.
ORIGINOFEUKARYOTES possible.Somegenetrees,thoselikeforglutaminesynthetase
(GS),glutamatedehydrogenase(GDH),andthe70-kDaheat
Threedifferentparalogousgenephylogenies(andarecently shockprotein(HSP70),positiontheArchaeaasaparaphyletic
published fourth rooting obtained by using carbamoyl-phos- groupwithintheBacteria.Inothergenephylogenies,likethose
phate synthetase [210]) provide a general consensus that the for glyceraldehyde-3-phosphate dehydrogenase (GAPDH), 3-
rootoftheuniversaltreeliessomewhereintheBacteria,thus phosphoglyceratekinase(PGK),andenolase,theBacteriaand
positioningArchaeaandeukaryotesassistergroups.However,
eukaryotesclustertogether.AswithrRNA,anyuniversaltree
there is still uncertainty about this rooting, since each dupli-
rooting based on a single gene can be inferred only by the
cated gene data set has its own particular, and significant,
midpointmethod,whichsimplyplacestherootsomewherein
shortcomings. Furthermore, three or four genes spanning a
thecenterofthetree,asnearlyequidistantfromallorganisms
few thousand base pairs may not be representative of entire
as possible. There is also a critical question of how well a
genomeswiththousandsofgenesand,atleast,severalmillion
particulargenetreereflectstheactualevolutionoftheorgan-
basepairs.
isms.Horizontalgenetransferandlineage-specificdifferences
TherearemanypropertiesthatmakerRNAasuitablemo-
in evolutionary rates could result in a gene tree radically dif-
lecularmarkerforphylogeneticreconstruction:itoccursinall
ferentfromthespeciesphylogeny.
livingorganisms,itssequencesarehighlyconserved,andthere
Just how widespread these phylogenetic distortion effects
is no compelling evidence for interspecific transfers of rRNA
areandtowhatextenttheyhaveaffectedparticulargenetrees
genes.However,eventhemonophylyofArchaea,Bacteria,and
are important issues to molecular evolution. Developing evo-
eukaryotes, as strongly suggested by rRNA trees, is open to
challenge.ThehigherG1CcontentofrRNAgenesofcertain lutionary theories solely on the basis of any single gene phy-
logenyis,atbest,highlyspeculative.However,ifthemajority
organisms,suchasthermophilicmembersoftheArchaeaand
Bacteria, could be biasing phylogenetic reconstruction, and ofgenetreesdocorrectlyreflectthecorrectevolutionaryori-
new environmental PCR-amplified rRNA sequences have in ginsfordifferentbitsofthegenome,onemightconcludethat
some instances reduced the overall statistical support for ar- thedescentoftheBacteria,Archaea,andeukaryotesfromthe
chaeal monophyly (15). More critically, there are growing cenancestorinvolvedamorecomplexseriesofgeneticevents.
numbersofproteingenephylogenieswhichchallengetheno- In this vein, Sogin (304) and Zillig et al. (343, 344) theorized
tion of monophyletic domains and, indirectly, Archaea-eu- thattheeukaryoticcelldidnotdirectlyevolvefromanarchaea-
karyotesisterhood. like ancestor but, rather, that the eukaryotic nucleus arose
The various universal protein gene phylogenies have been fromthecellularfusionbetweeneitherabacteriumor“proto-
summarized previously (94, 134), and the further elaboration eukaryote”andanarchaeon(Fig.2D).
of this list is an important aspect of this review (Fig. 4). It Sogin’s (304) version adheres to the initial conceptions of
seems that all combinations of domain branching orders are WoeseandFoxofthecenancestorasaprogenote(anorgan-
VOL.61,1997 ARCHAEA AND THE PROKARYOTE-TO-EUKARYOTE TRANSITION 463
andSingh(147)suggestedthatitwasaneocyte.Boththeories
suggest that any genome fusion event occurred prior to the
widelyacceptedbacterialendosymbiosisleadingtointracellu-
larorganelles,suchasplastidsandmitochondria.
Collectively, the theories of Sogin (304) and Zillig et al.
(344)havebeenreferredtoasthechimericorfusionhypoth-
esisoftheoriginoftheeukaryoticgenome,althoughthever-
sionofZilligetal.hasbeenmorewidelyconsidered(134).This
terminology is somewhat confusing since the chimeric nature
oftheeukaryoticcellhasbeenlongrecognizedwithrespectto
theendosymbioticoriginoforganelles(reviewedinreference
137). In addition, it has been established that the eukaryotic
genomeisachimerawheregenesofancienteukaryoticances-
try coexist with genes more recently acquired from bacterial
endosymbionts.Inthecontextofthisreview,theterm“chime-
ra hypothesis” will be applied to suggestions that the eukary-
otic genome originated from a fusion between two indepen-
dent, noneukaryotic genomes, while the term “archaeal
hypothesis”willrefertothemoreconventionalview,i.e.,that
eukaryotesandtheArchaeadivergedrecentlyfromacommon
ancestor.
Unfortunately,therearefewobjectivecriteriafortherejec-
tion or acceptance of any of the chimera hypotheses. These
hypotheses predict a mixture of phyletic relationships among
different gene families which is self-evident. Other explana-
tionsfortheobservedmixingofdomainrelationships,suchas
unequalmutationrates,hiddengeneparalogy,andhorizontal
genetransfers,cannotbestrictlyruledout.Furthermore,only
verybroadspeculationcanbemadeaboutpossiblecandidates
for cell fusion participants. Although bacteria living intracel-
lularlyinadifferentbacterialspecieshavebeenreported(209),
phagocytosis by a bacterium has never been observed. Nor is
thereanyevidencefortheexistenceofthesophisticatedRNA-
based organisms with cytoskeletons integral to Sogin’s proto-
eukaryotic model. On the other hand, the endosymbiosis
hypothesis,clearlyestablishesa-proteobacteriaandcyanobac-
FIG. 4. Alternativerootingsoftheuniversaltreeandthesingle-proteingene
phylogeniesthatsupportthem.Individualgenetreesandabbreviationsaregiven teriaastherespectiveprogenitorsofmitochondriaandplastids
inthetext. (chloroplasts).
Nonetheless, the version of the chimeric hypothesis pro-
posed by Zillig et al. (344) has found some interest and sup-
ism where the genotype and phenotype were more loosely port.Overthepast20yearsfollowingWoese’sinitialuniversal
coupled than today [338]) from which two cellular lineages rRNA trees, many archaeal protein-coding genes have been
emerged: one composed of prokaryotic, DNA-based organ- sequencedthatarehomologoustocounterpartsintheBacteria
isms (the Bacteria and Archaea) and the other composed of and eukaryotes. Golding and Gupta (134) constructed un-
sophisticated RNA-based organisms (the putative proto-eu- rooted phylogenetic trees for 24 protein genes which were
karyote).Subsequently,theArchaeaandBacteriadivergedbe- common to all three domains. They found that nine of the
fore the engulfment of an archaeon by the proto-eukaryote. proteinsgavestatisticallysignificantsupportforthemonophyly
Theproto-eukaryotewasproposedtohavehadarudimentary of domains (sensu Woese’s rRNA trees) and the closer asso-
cytoskeleton,sincesuchaninnovationwouldbenecessaryfor ciation of the Archaea and eukaryotes (by midpoint rooting).
phagocytosis. The engulfed archaeon formed the cell nucleus However, seven of the protein gene trees supported an alter-
which led to the replacement of the host RNA genome by a nativetopologywithtwoclades,oneofgram-positivebacteria
DNA-basedone.Soginsuggestedthatcontradictionsbetween and the Archaea, and the other of “gram-negative” bacteria
rRNAphylogenies,whichshowcontemporarytheArchaeaand and eukaryotes. The remaining eight protein trees were not
Bacteria as most similar, and paralogous protein gene trees, statistically significant. Golding and Gupta stated that their
which show Archaea and eukaryotes as sister groups, exist results supported “the hypothesis of a chimeric origin for the
becauseeukaryoticrRNAisaremnantoftheproto-eukaryote eukaryotic cell nucleus formed from the fusion of an archae-
genome. bacteriaandagram-negativeBacteria.”
Zilligetal.(344)similarlyproposedthatseparatelineagesof Such a conclusion is probably premature since new se-
theArchaeaandBacteriadescendedfromthecenancestorbut quences can radically alter gene trees. If the full range of
that eukaryotes did not exist until a cellular fusion occurred availablesequencesareconsidered,noneofthesevenprotein
betweenspeciesfromthetwoprokaryoticgroups.Thismodel, gene trees support the monophyletic groups of gram-positive
unlikethatofSogin(304),hasthecenancestorasagenote,a bacteria and the Archaea or gram-negative bacteria and eu-
prokaryotewithafullyfunctionalgenome,ratherthanaprog- karyotes (281). These gene trees, which include asparatate
enote. Gupta and Golding (144) have elaborated upon the aminotransferase (AAT), GS, GDH, HSP70, histidinol phos-
hypothesis of Zillig et al. in proposing that it was a gram- phate synthetase, and pyrroline 5-carboxylate reductase, are
negative bacterium that engulfed an archaeon; later, Gupta described in more detail below. (Eukaryotic isoforms of the
464 BROWN AND DOOLITTLE MICROBIOL.MOL.BIOL.REV.
FIG. 5. The70-kDaheatshockprotein(HSP70)genephylogeny.Cytostolic(Cyto.)andendoplasmicreticulum(E.R.)eukaryoticisoformsareindicated.
seventhgene,ferredoxin,occuronlyinplantsandhaveprob- karyotes. However, a universal phylogeny based on HSP70
able plastid/cyanobacterial origins.) Recently, Gupta and suffers the same drawbacks of any single-gene tree, in that it
Golding derived phylogenetic trees of phosphoribosylformyl- cannotbeuniquelyrooted.Sincetherootingissubjective,the
glycinamidinesynthetase(FGAMsynthetase)whichclustered twoclusteringpossibilitiesforthecladeofgram-negativebac-
gram-positive bacteria and the Archaea, on one hand, and teria,eitherwitheukaryotesorwithgram-positivebacteriaand
proteobacteriaandeukaryotesontheotherhand(145).How- Archaea,haveequalvalidity.Inaddition,itisdifficulttoeval-
ever, subsequent analyses showed that the cyanobacterium uate the proposition that eukaryotes arose from the specific
Synechococcous also clusters with the group of gram-positive fusionofanarchaeon“eocyte”withagram-negativebacterium
bacteriaandArchaea(281). since HSP70 gene sequences from Crenarchaeota are un-
Guptaetal.haveextensivelyusedHSP70genephylogenies known.
as support for the chimeric origin of eukaryotes hypothesis According to Gupta et al., the earliest divergence was that
(143–147). HSP70 genes from the Archaea and gram-positive separatinggram-positivebacteriaandtheArchaea,yetallphy-
bacteriaareclearlymoresimilar,withrespecttobothphylog- logenetic treatments of HSP70 genes show these groups as
eny (Fig. 5), and the absence of a specific 25-amino-acid se- paraphyletic rather than monophyletic (whereas eukaryotes
quence found in HSP70 genes of other bacteria and eu- and all other bacteria can be resolved as separate monophy-
VOL.61,1997 ARCHAEA AND THE PROKARYOTE-TO-EUKARYOTE TRANSITION 465
leticgroups).Theysuggestedthattheintermixingofarchaeal The GenBank, SwissProt, and PIR databases were initially
species with those of gram-positive bacteria and the Archaea searched (up to January 1996) for all archaeal entries (which
reflectedpastpatternsofalternativelyevolvinglineages.How- werethemostlimiting);thiswasfollowedbydownloadingall
ever, if such stochastic processes were involved in the early possible bacterial and eukaryotic orthologs. Excluded were
evolutionofthisHSP70gene,thestatisticalreliabilityoflater tRNA and rRNA genes, gene families for which eukaryotic
branchingpointsisalsoopentodebate.Furthermore,torec- versions only exist in organellar genomes, and partially se-
onciletheobservedHSP70genephylogeny,onewouldhaveto quenced genes. Of course, with the generation of new se-
postulatetheunlikelycaseofarapidaccelerationinmutation quenceentriesproceedingatanever-acceleratingpace,sucha
rates in eukaryotes while gram-positive bacteria and the Ar- survey can only aspire to be a static picture or “snapshot” of
chaea evolved so slowly as to appear similar to each other the global database at one particular moment. For example,
(281). shortly after most of these gene phylogenies were compiled,
thecompletegenomesequenceofthethermophilicmethano-
genM.jannaschiiwasreleased(49),andduringtherevisionof
UNIVERSALPROTEINGENETREES
this paper, the publication of the Archaeoglobus fulgidus ge-
nome (161a) was pending. For the most part, these new se-
MethodsandCaveats
quenceswerenotincludedintheanalysis,althoughthenum-
Sequences.Completegenomesarebeingsequencedfroman berofgenefamiliesavailabletoderiveuniversaltreeshasbeen
ever-increasing number of bacterial, archaeal, and eukaryotic dramatically increased. However, it is unlikely that these new
species. This flood of DNA sequence data brings new chal- archaeal sequence data would have greatly changed the pre-
lenges and opportunities to the field of evolutionary biology sentedgenetreetopologies,sincespeciesofEuryarchaeota,in
(41).Inthiscontext,thecomparativeanalysisofmanyindivid- particularmethanogens,arewidelyrepresented.
ualuniversalgenetrees,suchasthatinitiatedbyGoldingand Considered here are the phylogenies of over 60 universal,
Gupta (134), has value as a tentative, conceptual framework orthologousproteinswhicharerepresentedbyover1,200dif-
fortheevolutionaryanalysesofgenomes.Ratherthanrelying ferentsequences.Oftheseproteins,21arecomplexedwiththe
ontheselectionandinterpretationofasinglegenephylogeny, ribosome. Despite the large size of this data set, there were
a combined analysis of multiple gene trees might arrive at someseriouslimitationswithrespecttospeciesdiversity.Less
some broader consensus picture of the universal tree. This than15%ofthesequencesarefromtheArchaea.Fewproteins
analysis could be extended to search for possible correlations are available from protist groups that branch deeply in eu-
between gene phylogenies, cellular functions, and suggested karyotes,suchasMetamonda,Microsporidia,andParabasalia
species relationships. Later, when more genomes have been (Fig.1).Inaddition,thebacterialsampleisbiasedtowardthe
sequenced, the spatial arrangement of genes might also be best-known species, namely, E. coli, Bacillus subtilis, Hae-
considered. mophilus influenzae (117), and Mycoplasma genitalium (124).
The remainder of this review will summarize the interdo- The degree of representation from evolutionarily diverse
mainrelationshipsimpliedbydifferentuniversalproteingene groups is an important consideration in the interpretation of
trees. The phylogenies of some of these proteins have been any“global”phylogeneticanalysis.
well studied previously, while others are shown here for the Phylogeneticmethods.Priortophylogeneticanalyses,amino
first time (to the best of our knowledge). The discussion of acid sequences from orthologous genes were aligned by the
these gene trees will be structured around the generalized program MULTALIN (72) with the BLOSUM62 amino acid
metabolicpathwaysinwhichtheencodedenzymesparticipate. substitutionmatrix(153)andagappenaltyof20.Asnecessary,
Riley (277) provided a useful framework for the biochemical sequencealignmentswerevisuallyeditedwithpreviouslypub-
classification of gene products in E. coli, which will be very lished alignments as guides, and all gap positions were re-
looselyadaptedhere.However,asRileyherselfpointsout,the moved prior to phylogenetic analyses. To estimate the evolu-
assignmentofcertainenzymestoparticularfunctionalcatego- tionary distance, pairwise distances between all taxa were
ries can be arbitrary. For instance, carbamoyl phosphate syn- calculated with the program PROTDIST (from the PHYLIP
thaseservesinbothpyrimidineandargininebiosynthesis,and 3.57 package [114]), which estimates the number of expected
so this gene phylogeny is arbitrarily included with those of amino acid replacements per site by using a model based on
other amino acid biosynthetic enzymes largely out of conve- the Dayhoff PAM substitution matrix (86). The resultant dis-
nience. Already discussed are two gene phylogenies, those of tance matrix was then used to draw a neighbor-joining tree
ATPasesubunits,categorizedasATP-protonmotiveforcein- (with the program NEIGHBOR). The statistical confidence
terconversionbyRiley(277),andHSP70,consideredhereasa foreachnodeinaparticulartreewasestimatedbybootstrap-
chaperoninwhileRileydesignateddnaKacomponentofDNA ping, which involves the generation of 100 multiple random
replication, restriction-modification, recombination, and re- subsets of the alignments with the program SEQBOOT, and
pair. subsequentlyrecalculatingthedistancematricesandneighbor-
Phylogenetic analyses were conducted only on gene se- joiningtrees.Inthefigures,onlynodefrequenciesgreaterthan
quences judged to be homologous rather than paralogous or 50%arereported.
analogous(217).Theelongationfactors,ATPasesubunits,and Thegenetreesdepictedhereareonlyroughapproximations
aminoacyl-tRNA synthetases are all examples of paralogous of species relationships. More complete and precise phyloge-
gene families. Here, interdomain distances and gene trees neticanalysiswouldentailagreaternumberofbootstraprep-
were determined only among orthologous genes within these lications and use a variety of different methods such as maxi-
larger families of genes. An example of analogous genes are mum parsimony and maximum likelihood. Furthermore, the
the DNA ligases, which are known for the Archaea, Bacteria, rootingofanyuniversaltreebasedonasinglegenecanonlybe
and eukaryotes and perform similar functions in each organ- implied—usually in the longest branch leading to the most
ism. However, bacterial ligases show no meaningful sequence distantly related domain. However, a midpoint rooting is not
similarities to archaeal or eukaryotic ligases (193), thus ren- necessarilythecorrectone.Forexample,isoleucyl-tRNAsyn-
dering it impossible to use these genes to derive meaningful thetases of the Archaea and Bacteria have slightly higher se-
evolutionaryrelationshipsamongthethreedomains. quence similarity, but with the inclusion of paralogous valyl-