1 Letter An ACP-independent fatty acid synthesis pathway in archaea?

12 Pages·2012·0.38 MB·English

An ACP-Independent Fatty Acid Synthesis Pathway in Archaea:
Implications for the Origin of Phospholipids
Jonathan Lombard, Purificacio´n Lo´pez-Garc´ıa, and David Moreira*
Unite´d’Ecologie,Syste´matiqueetEvolution,Universite´Paris-Sud,Orsay,France
*Correspondingauthor:E-mail:[email protected].
Associateeditor:AndrewRoger
Abstract
Fattyacids(FAs)aremajorbuildingblocksofmembranephospholipidsinbacteriaandeukaryotes.Theirpresumedabsencein
archaea led to propose a late origin in bacteria and eukaryotes and that the last common ancestor of living organisms (the
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cenancestor)wasdevoidofbothFAandphospholipidmembranes.However,smallFAamountsandhomologsofbacterialFA o
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biosynthesis enzymes are found in archaea. We have investigated the origin of these archaeal enzymes using phylogenomic n
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analysesofallenzymesofthemainbacterialFAbiosynthesispathway.Ourresultssuggestthatmodernarchaeaandtheirlast ad
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commonancestorpossessedacompletepathwayexceptfortheacylcarrierprotein(ACP)processingmachinery,whichevolved d
inthebacteriallineage.Thishasnotonlyimplicationsforarchaealphysiologybutalsoopensthepossibilityforthepresenceof fro
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ACP-independentFAsynthesisinthecenancestor,whichmayhavebeenendowedwithFA-phospholipidmembranes. h
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Keywords:fattyacidsynthesis,acylcarrierprotein,archaea,earlyevolution,cenancestor. s://a
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Althoughfattyacids(FAs)playmajorrolesasstoragemole- Determining the evolutionary origin of archaeal FA has m
cules, secondary metabolites, and components of bacterial implications both to envisage early evolution scenarios and ic.o
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and eukaryotic membrane phospholipids, little is known to better understand archaeal physiology. FA biosynthesis p
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abouttheminarchaea.Thisreflectsthat,mostoften,archaeal occurs through repetitive condensation of acyl (malonyl- o
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membrane phospholipids are considered to lack FA and to CoA) groups in a series of cyclic steps (fig. 1) catalyzed by /m
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carry isoprenoids instead (Boucher 2007). In fact, although enzymesthatmaybeindividual(FAsynthasetypeII[FAS-II]) e
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bacterial and eukaryotic phospholipids contain FA bound orfusedinoneuniquepolypeptide(FAS-I).FAS-IIisthemain rtic
to sn-glycerol-3-phosphate with ester links, in archaea, iso- FAbiosynthesispathwayinmostbacteria,mitochondria,and le
-a
prenoids are linked to sn-glycerol-1-phosphate through chloroplasts(Whiteet al.2005),whereasFAS-Iismorerarein b
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ether bounds (De Rosa et al. 1986; Boucher 2007). These bacteria but predominant in the eukaryotic cytoplasm tra
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striking differences figured among the main cellular charac- (Schweizer and Hofmann 2004). As we were particularly in- t/2
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teristicsthatsupportedarchaeaasanindependentdomainof terestedbythepresenceofFAShomologsinarchaeaandonly /1
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life(Woeseet al.1978). individual FAS-II but not polypeptidic FAS-I homologs were /3
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However, experimental data show that FAs also exist in detectedintheavailablearchaealgenomesequences,were- 1
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archaea. Biochemical evidence for FA synthase machineries movedtheFAS-Isequencesfromouranalysesandrestricted 1
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(Pughet al.1971;PughandKates1994)andsmallamountsof oursystematicphylogenomicanalysestotheFAS-IIindividual 8
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free FA or their derivatives (Kates et al. 1968; Langworthy peptides.Ourresultssupportthattheactualdistinctivefea- 3 b
et al. 1974; Tornabene et al. 1978; Carballeira et al. 1997; turebetweenarchaeaandbacteriaisnotthepresenceofthe y g
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Nishiharaet al.2000)havebeenreportedindiversearchaea. FASsystemitself,butthelackoftheFAS-relatedacylcarrier e
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PhospholipidsbearingFAhavebeendetectedinverydiverse protein(ACP)processingmachineryinarchaea. t o
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euryarchaeotes(Gattingeret al.2002),and,asinbacteriaand 1
FAS-II Homologs in Archaea 8
eukaryotes, archaeal FAs are sometimes involved in protein L N
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structure(Colellaet al.1998)andacylation(PughandKates Inbacteria,severalreactionssupplythemalonyl-ACPbuilding tve
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1994).Finally,archaealhomologsofbacterialFAbiosynthesis blocks necessary to FAS-II: 1) acetyl-coenzyme A (CoA) is tb
ee
enzymes have been reported in archaeal genomes (Pereto´ converted into malonyl-CoA by the acetyl-CoA carboxylase rr 2
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et al. 2004; Iverson et al. 2012). Despite these arguments, (ACC),2)aphosphopantetheinegroupfromCoAisattached 1
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thesignificanceofFAinarchaea(includingthelastarchaeal by an ACP synthase (ACPS) to the apo-ACP, and 3) the
commonancestor[LACA])remainspoorlyacknowledgedin malonyl-CoA:ACP transacylase (MCAT) charges malonyl-
recentscientificliterature(Boucher2007;Dibrovaet al.2011). CoA to holo-ACP (fig. 1). A wide diversity of archaea bear
Similarly, the assumption that the last commonancestorof ACC homologs of possible monophyletic origin, suggesting
livingorganisms(thecenancestor)lackedFAhasevenserved theirverticalinheritancefromthecenancestor(Lombardand
asasupplementaryargumenttoproposethatthisorganism Moreira 2011a). ACP is a peptide cofactor that covalently
could not synthesize phospholipids and, therefore, was binds all FA intermediates, channeling them among the
devoidoflipidmembranes(MartinandRussell2003). FAS-II enzymes. Except for a few unrelated species that
(cid:2)TheAuthor2012.PublishedbyOxfordUniversityPressonbehalfoftheSocietyforMolecularBiologyandEvolution.Allrightsreserved.Forpermissions,please
e-mail:[email protected]
Mol.Biol.Evol.29(11):3261–3265 doi:10.1093/molbev/mss160 AdvanceAccesspublicationJune19,2012 3261
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Lombardet al. . doi:10.1093/molbev/mss160
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FIG.1. ArchaealhomologsofthearchetypicalbacterialFAS-IIpathway.ThebacterialFAS-IIenzymesarerepresented.ProteinnamesandECnumbers fro
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areindicatedwithinboxes.Blackboxesindicatetheexistenceofarchaealhomologs,potentiallyinvolvedinanalternativearchaealCoA-dependent h
pathway,whereasgrayboxesdenotebacterialenzymesabsentinmostarchaea.ACC,acetyl-CoAcarboxylase;ACP,acyl-carrierprotein;ACPS,acyl ttp
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carrierproteinsynthase;CoA,coenzymeA;DH,beta-hydroxyacyldehydratase;ER,enoylreductase;KAS,beta-ketoacylsynthase;KR,beta-ketoacyl ://a
reductase;MCAT,malonyl-coenzymeA:acyl-carrier-proteintransacylase. c
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probably acquired ACP by independent horizontal gene and 4) universally distributed HMGS. Thiolase and HMGS u
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transfers (HGTs), we did not retrieve homologs of the sequences supported the separation of most bacterial and .co
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ACP-processing machinery (ACP, ACPS, and MCAT) in ar- archaeal sequences into two monophyletic groups, strongly /m
chaea.Thiscontrastedwiththepresenceofhomologsofall suggestingthatthecenancestorwasendowedwiththesetwo be
the other FAS genes in a large diversity of archaea (supple- enzymes. In contrast, KAS is widespread in bacteria and /artic
mentarytableS1,SupplementaryMaterialonline). absentinarchaea.ThiolasesandHMGScatalyzetheremoval le
Once malonyl-ACP is produced, it is condensed with ofanacetyl-CoAmoietyfromanacyl-CoAchainortheop- -ab
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acetyl-CoA (beta-ketoacyl synthase III [KAS III], FabH) to posite condensation reaction, so the major difference tra
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yield ketoacyl-ACP, an intermediate that is sequentially re- betweenKASandtheseotherenzymesistheuseofsubstrates t/2
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duced (beta-ketoacyl reductase [KR], FabG), dehydrated linkedtoACPinsteadofCoA.Thus,ourresultssupportthat /1
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(beta-hydroxyacyldehydratase[DH],FabZorFabA),andre- the cenancestor was able to (de)acetylate acyl-CoA chains, /3
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duced again (enoyl reductase [ER], FabI). A subsequent ex- whereastheuseofacyl-ACPseemstobeamorerecentbac- 6
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tensionwithmalonyl-ACP(beta-ketoacylsynthasesKASIor terialderivedcharacter. /1
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II, respectively, FabB and FabF) conducts a new elongation WeobtainedsimilarresultsonKRsequencesthat,together 3
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cycle(fig.1).Althoughnonhomologousreplacementsexistin with ER, belong to the short-chain dehydrogenases/reduc- 73
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some bacteria (Marrakchi et al. 2003), we have focused our tasessuperfamily(Kallberget al.2002).Asthisfamilyisvery y
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searchonthemostcommonarchetypalFAS-IIenzymes. diverse, we reconstructed independent phylogenies for KR u
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A phylogenetic analysis of the thiolase superfamily, to and ER. The KR phylogeny incorporated the closely related t o
which KAS I, KAS II, and KAS III belong, has recently been PhaBacetoacetyl-CoAreductases,whichareinvolvedinpoly- n 1
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published(Jianget al.2008).Itseparatedthissuperfamilyinto hydroxyalkanoate (PHA) synthesis in bacteria and haloarch- N
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five clusters based on phylogenetic trees and active site ar- aea.ThemainenzymaticdifferencebetweenPhaBandKRis v
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chitecture:archaealthiolases,bacterial+eukaryoticthiolases, the use of CoA- instead of ACP-linked substrates, although m
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bacterial+eukaryoticKASI–KASII,archaealandeukaryotic some enzymes are known to use both (Taguchi et al. 1999; er 2
hydroxymethylglutaryl-CoA synthase (HMGS), and bacte- Ren et al. 2000). Although PhaB sequences were scattered 0
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rial+eukaryotic KAS III-chalcone synthases (CHS). However, amongKRhomologs,thebacterialKR-PhaBsequencesclus-
this can be questioned as only one very divergent archaeal teredaccordingtomainbacterialphyla(fig.2).Somearchaeal
sequencewasusedasanoutgroup,andHMGSwasrecently sequences were dispersed among the bacterial KR-PhaB, in-
showntobeuniversalandprobablypresentinthecenances- dicating independent HGTs from bacteria. Nevertheless, a
tor (Lombard and Moreira 2011b). Thus, we carried out a wide diversity of uncharacterized archaeal sequences
more complete analysis of the thiolase superfamily (supple- branched at the base of the bacterial KR-PhaB cluster.
mentary fig. S1, Supplementary Material online). Although Maximum likelihood (ML) phylogenetic reconstruction of
these enzymes preserve strong structural similarity, primary these archaeal sequences showed at least two paralogs in
sequence conservation is low. However, similarities within crenarchaeota (with some HGTs from them to other
each group of sequences point to four different clusters groups),sistersofabasalgroupofeuryarchaeota(supplemen-
withdistinctiveenzymaticfunctions:1)universallydistributed taryfig.S2,SupplementaryMaterialonline).Thisresultindi-
thiolases,2)bacterialKASI–KASII,3)bacterialKASIII–CHS, catestheancientpresenceofthesegenesnotonlyinthelast
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FattyAcidBiosynthesisinArchaea . doi:10.1093/molbev/mss160
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FIG.2. Schematicrepresentationofthebeta-ketoacylreductases(KR)maximumlikelihoodphylogenetictreereconstructedusing569representative rtic
sequencesand187conservedsites(forthecompletetreeseesupplementaryfig.S2,SupplementaryMaterialonline).Numbersarebootstrapvalues. le
Blue, green, and orange branches correspond to bacterial, eukaryotic, and archaeal sequences, respectively. Stars and pentagons indicate -ab
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well-characterizedKRandPhaBenzymes,respectively.Trianglespointtoenzymescarryingbothfunctions. tra
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/1
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common ancestor of the crenarchaeota but likely also in Conclusion /3
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LACA. The proximity to the KR-PhaB group suggests that 6
these archaeal sequences may catalyze similar reactions Except for some rare cases of HGT of ACP-processing ma- 1/1
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chineryenzymesfrombacteria,theseenzymesarecompletely 5
(probablyonCoA-linkedsubstrates,ACPbeingabsentinar- 3
chaea). As for KR, the ER phylogeny supported the mono- absentfromarchaea,incontrastwiththepresenceofallother 873
phyly of most bacterial sequences and revealed two FAS-II enzymes. Moreover, all phylogenies of FAS enzymes by
supportthatarchaealsequencesaremorecloselyrelatedto g
basal-branchingER-likeparalogsincrenarchaeota,indicating u
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SanupapnlecmienetntdauryplMicaattieornialinontlhinise)g.rHoGupTs(sfruopmplcermenenartcahryaefiogt.aSt4o, tbhaacntetroialeennzzyymmeessuascitninggAoCnPF-lAinSk-elidkessuubbsstrtaratetess.Tlinhkuesd,wtoeCporoA- st on 1
some euryarchaeota and bacteria could be noticed, but the pose that archaea should not be considered as completely 8 N
presenceofseveralbasal-branchingeuryarchaeotalsequences devoidoftheFASmachinerybutonlyoftheACP-processing ov
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supportedanancientoriginalsoinEuryarchaeota.Withthe system,whichseemstohavespecificallyevolvedinthebac- m
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eqxucireepdtiobny oHfGsTomfreomseqbuaecntecreisa,(Hmaolostbaacrctehraiaelaels)DpHrohboambloyloagcs- ttieornia,liltinseeaegme.sAlilktheolyutghhatthtishestsiellerenqzuymireessbaiocccohuemnticfaolrvtehreificFaA- er 20
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were closely related to mitochondrial DH and MaoC/PhaJ detectedinarchaea(Gattingeret al.2002).Fromabiochem- 8
enzymes (supplementary fig. S3, Supplementary Material icalperspective,recentworkshowingthatthechannelingof
online).MitochondrialDHactsonacyl-ACPchains,whereas FAintermediatesfromoneFAS-IIenzymetothenextinthe
MaoC/PhaJusesacyl-CoAsubstratesinPHAsynthesis(Tsuge cycle is permitted by unique ACP conformations (Ploskon
et al.2003;Autioet al.2008).Paralogscouldbedetectedin et al.2010)raisesthequestionofthebiochemicalmechanism
crenarchaeota, but their monophyly was difficult to asses ofthisputativearchaealFAS.Thepotentiallowerefficiencyof
becauseofthehighsequencedivergenceandsmallnumber an ACP-independent FAS could account for the small
of conserved alignment positions (112). Although the func- amounts of FA detected in archaea. From an evolutionary
tion of most archaeal enzymes remains unknown, they can perspective,thepresenceofacyl-CoAFAS-likemachineriesin
reasonably be assumed to carry out DH-type reactions on bothbacteriaandarchaeaarguesfortheexistenceofasimilar
CoA-linked substrates. In summary, our analyses suggest pathwayinthecenancestor,contrarytopreviousclaimsthat
thatLACAboreKR,ER,andpossiblyDHenzymes. thecenancestorlackedFA(MartinandRussell2003;Dibrova
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Lombardet al. . doi:10.1093/molbev/mss160
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