Beget­ting the Eu­karya: An Un­ex­pected Light

by Franklin M. Harold

Con­cern­ing the ori­gin of eu­kary­otic cells, much has been writ­ten but al­most every­thing re­mains to be set­tled. No one dis­putes that mi­to­chon­dria de­rive from free-liv­ing bac­te­ria that es­tab­lished an in­ti­mate sym­bi­otic re­la­tion­ship with a host of some kind and pro­gres­sively turned into or­ganelles, work­horses of me­tab­o­lism, and a hall­mark of eu­kary­otic or­ga­ni­za­tion. But con­sen­sus ends here; the na­ture of that host, the tim­ing and cir­cum­stances of the part­ner­ship, and its role in gen­er­at­ing the con­spic­u­ous com­plex­ity of eu­kary­otic cells all re­main elu­sive and en­tan­gled in con­tro­versy. In a com­pre­hen­sive re­view of the sub­ject pub­lished in 2006, Mar­tin Em­b­ley and William Mar­tin (6) con­cluded bleakly that the evo­lu­tion­ary gap be­tween prokary­otes and eu­kary­otes is now deeper, and the na­ture of the host that ac­quired the mi­to­chon­drion more ob­scure, than ever be­fore. No one will claim that the dark­ness has been lifted, but just in the past few years this in­tractable sub­ject has be­gun to ap­pear in a fresh light.

Peach Tree in Bloom by Vin­cent Van Gogh. Source

A good place to start is an ar­ti­cle by Mik­lòs Müller and nine co-au­thors in the June is­sue of MMBR (15). Un­less you are in the busi­ness, a meaty re­view of en­ergy me­tab­o­lism in anaer­o­bic eu­kary­otes may not set your pulse rac­ing; but if you are cu­ri­ous about the ori­gin of mi­to­chon­dria and their place in the his­tory of the eu­kary­otic cell, you will find here an ev­i­dence-based sum­mary of where that in­quiry stands. For present pur­poses, let me high­light just three points from that ar­ti­cle.

1. The di­ver­sity of eu­kary­otic en­ergy me­tab­o­lism is ex­tremely lim­ited, much nar­rower than that of prokary­otes. Most eu­kary­otes live by mi­to­chon­dr­ial res­pi­ra­tion with oxy­gen as the ul­ti­mate elec­tron ac­cep­tor, and gen­er­ate the bulk of their ATP by a chemios­motic pro­ton cir­cu­la­tion cou­pled to an ATP syn­thase. This path­way is sup­ple­mented by fer­men­ta­tive re­ac­tions in the cy­to­plasm linked to the clas­si­cal Em­b­den-Mey­er­hof scheme of gly­col­y­sis. Anaer­o­bic eu­kary­otes lack­ing con­ven­tional res­pi­ra­tion are wide­spread, rep­re­sented by over a thou­sand species. In these, ATP is pro­duced by sub­strate-level phos­pho­ry­la­tion, chiefly by the de­car­boxy­la­tion of pyru­vate, which is com­monly as­so­ci­ated with mi­to­chon­dria or their evo­lu­tion­ary rel­a­tives. The path­ways of eu­kary­otic en­ergy me­tab­o­lism, in­clud­ing the anaer­obes, are all very much the same; the par­tic­i­pat­ing en­zymes rep­re­sent a sub-set of a eu­kary­otic com­ple­ment that was prob­a­bly al­ready present in LECA, the last eu­kary­otic com­mon an­ces­tor.

2. All con­tem­po­rary mi­to­chon­dria ap­pear to share a com­mon an­ces­try from among the al­pha-pro­teobac­te­ria. The clos­est liv­ing rel­a­tives of that puis­sant sym­biont are thought to be fac­ul­ta­tive anaer­obes such as Rho­dospir­il­lum rubrum and Rhodobac­ter cap­su­la­tum, ca­pa­ble of grow­ing by res­pi­ra­tion, fer­men­ta­tion or even pho­to­syn­the­sis, as cir­cum­stances re­quire. The ge­nomic ev­i­dence sug­gests that all ex­tant mi­to­chon­dria de­scended from a sin­gle episode of sym­bio­sis, a unique event in the his­tory of life.

3. All eu­kary­otes that have been ex­am­ined in suf­fi­cient de­tail, a sam­ple that now in­cludes rep­re­sen­ta­tives of all six su­per­groups, con­tain ei­ther stan­dard mi­to­chon­dria or or­ganelles re­lated to mi­to­chon­dria by de­scent. That tribe now in­cludes anaer­o­bic mi­to­chon­dria (whose res­pi­ra­tory chain ter­mi­nates in an en­doge­nously-pro­duced elec­tron ac­cep­tor such as fu­marate), a va­ri­ety of hy­drogeno­somes (en­ergy-gen­er­at­ing or­ganelles that lack res­pi­ra­tory chains, pro­duce ATP by sub­strate-level phos­pho­ry­la­tion, and typ­i­cally gen­er­ate hy­dro­gen gas as a by-prod­uct), and mi­to­somes (highly re­duced, mem­brane-bound com­part­ments that have no role in en­ergy trans­duc­tion). The strong im­pli­ca­tion is that mi­to­chon­dria are not an op­tional ac­ces­sory to eu­kary­otic cells but part of their ba­sic fab­ric.

Taken to­gether, these find­ings (and oth­ers omit­ted from this con­densed sum­mary) sup­port a co­her­ent the­sis, one that de­parts quite rad­i­cally from the "stan­dard model" (5). Un­til about a decade ago, the gen­eral pre­sump­tion was that the es­sen­tial fea­tures of eu­kary­otic or­ga­ni­za­tion evolved au­to­ge­nously in a proto-eu­kary­otic lin­eage, with­out con­tri­bu­tions from other or­gan­isms. The sym­bionts that even­tu­ally be­came mi­to­chon­dria would have been ac­quired, prob­a­bly by phago­cy­to­sis, by a host that al­ready pos­sessed the es­sen­tial char­ac­ter­is­tics of eu­kary­otic cells in­clud­ing a nu­cleus, en­domem­branes and a cy­toskele­ton (1, 4, 11). This en­tity has been dubbed the "prim­i­tive phago­cyte". Müller et al., and many oth­ers (see be­low), ad­vo­cate a dif­fer­ent take on the gen­e­sis of the eu­kary­otic or­der. At an early stage in the evo­lu­tion of what would be­come the eu­kary­otic cell, a fac­ul­ta­tive bac­terium akin to today's al­pha-pro­teobac­te­ria forged an in­ti­mate as­so­ci­a­tion with a host whose na­ture is left open (but see be­low). By then, the di­ver­si­fi­ca­tion of the bac­te­ria must have been well un­der­way. Oxy­gen had be­gun to ac­cu­mu­late, at least lo­cally, but the at­mos­phere and the oceans were still largely anaer­o­bic (and would long re­main so). A date around two bil­lion years ago seems a fair guess. That was a fate­ful en­counter, quite pos­si­bly a unique event. The sym­biont con­tributed many genes to the con­sor­tium, and set it on track to evolve greater com­plex­ity, au­ton­omy and so­phis­ti­ca­tion than any­thing known in the prokary­otic uni­verse.

What was it about sym­bio­sis that made so huge a dif­fer­ence? As out­lined in an ear­lier con­tri­bu­tion to this blog (21), I have been im­pressed by the the­sis of Lane and Mar­tin (12) that it's ba­si­cally about en­er­get­ics: thanks to its many com­part­men­tal­ized en­ergy packs, de­rived from the sym­biont, the con­sor­tium could mo­bi­lize far more en­ergy per gene than could a prokary­otic cell. En­ergy ga­lore sup­ported ex­pan­sion of the genome, which in turn un­der­pinned ris­ing size and com­plex­ity. So we have two very dif­fer­ent nar­ra­tives of the ori­gin of mi­to­chon­dria, and of the cells that har­bor them. In one, sym­bionts come late into ad­vanced proto-eu­kary­otes; in the other, they come early and help shape the eu­kary­otic or­der.

It takes at least two to make a re­la­tion­ship. Who, then, was the part­ner that hosted the pre­cur­sor of mi­to­chon­dria? That is­sue con­tin­ues to be­devil the en­tire field of cell evo­lu­tion, with ad­vo­cates and ev­i­dence to sup­port al­most every con­ceiv­able an­swer.

Carl Woese and col­leagues (16,18) taught us all that the nu­clear lin­eage of eu­kary­otes is one of three pri­mary lines of de­scent, a sis­ter-clade to the Ar­chaea, whose roots reach back al­most as far as the last com­mon an­ces­tor of all cel­lu­lar life. Thomas Cav­a­lier-Smith has ar­tic­u­lated and tena­ciously de­fended the the­sis that the elu­sive host orig­i­nated from the Eu­bac­te­ria, un­der­go­ing a se­ries of trans­fig­u­ra­tions that even­tu­ally gave rise to both Ar­chae­bac­te­ria and to the proto-eu­kary­otic phago­cyte. And mol­e­c­u­lar bi­ol­o­gists in­creas­ingly fa­vor the propo­si­tion that the eu­kary­otic line is fun­da­men­tally chimeric, orig­i­nat­ing in a sym­bi­otic as­so­ci­a­tion be­tween two prokary­otic cells, one bac­te­r­ial and the other ar­chaeal. De­pend­ing on whom you read, that may have hap­pened once or on sev­eral oc­ca­sions, with the ar­chaeon var­i­ously the donor of the consortium's ge­netic core, its nu­cleus, much of the cy­to­plasm or all of the above. To cite but one much-dis­cussed ex­am­ple, William Mar­tin and Mik­lòs Müller (14) pro­posed a syn­trophic as­so­ci­a­tion in which a fac­ul­ta­tive anaer­o­bic eu­bac­terium, pro­duc­ing hy­dro­gen gas, sus­tained a methanogenic ar­chae­bac­terium; they also spelled out a se­quence of tran­si­tions that would have turned that part­ner­ship into a eu­kary­otic cell. A decade ago, one ex­pected the ris­ing tor­rent of ge­netic and phy­loge­nomic ev­i­dence to ren­der a clean ver­dict. That did not hap­pen, leav­ing a pal­pa­ble sense of frus­tra­tion (8).

Con­tro­versy is the lifeblood of sci­ence, and some­times its bane too. But sci­en­tific dis­pu­ta­tions are sel­dom bat­tles to the death. More of­ten than not, they find res­o­lu­tion in a syn­the­sis that draws on the in­sights of sev­eral pro­tag­o­nists but tran­scends them all, and that may be hap­pen­ing now with re­gard to the elu­sive eu­kary­otic host. Move­ment be­gins with the provoca­tive find­ing from Mar­tin Embley's lab­o­ra­tory (3) that the phy­loge­nomic re­la­tion­ship be­tween eu­kary­otes and prokary­otes de­pends on the par­tic­u­lar sta­tis­ti­cal model em­ployed to an­a­lyze it. Ri­bo­so­mal RNA data have long been the main­stay of the con­ven­tional triple-stemmed tree of life, with the Eu­karya as one of the pri­mary lin­eages (Fig. 1A). But when the se­quences are in­ter­ro­gated us­ing the lat­est and most so­phis­ti­cated pro­ce­dures, they show some­thing quite dif­fer­ent: data from both rRNA and highly con­served pro­teins in­di­cate that eu­kary­otes branch from within the Ar­chaea, and are specif­i­cally re­lated to the phy­lum Cre­nar­chaeota. A sim­i­lar con­clu­sion was reached by Eu­gene Koonin's team (20): they have eu­kary­otes aris­ing as an early branch of the Ar­chaea, an un­known and pos­si­bly ex­tinct lin­eage that di­verged prior to the ra­di­a­tion of Ar­chaea into their con­tem­po­rary forms.

Such claims will sur­prise many but not James Lake, who first in­ferred a spe­cific re­la­tion­ship be­tween eu­kary­otes and "Eo­cytes" (=Cre­nar­chaeota) a quar­ter of a cen­tury ago, and has main­tained that po­si­tion ever since (17). His "ring of life" (Fig. 1B) has long been over­shad­owed by the three-do­main tree of life, and if it rested solely on phy­loge­nomic analy­sis would still be viewed with some sus­pi­cion. (My gen­er­a­tion, at least, un­der­stands that sta­tis­tics are like a bikini: what they re­veal is in­ter­est­ing, what they con­ceal is vi­tal.) But all of a sud­den, con­fir­ma­tion has be­gun to pop up from other quar­ters, too. Most no­table is the dis­cov­ery of true or­thologs of actin, ap­par­ently in­volved in cell mor­pho­gen­e­sis, in both Ther­mo­pro­teales (an or­der of Cre­nar­chaeota) and in Ko­rar­chaeota (7,9), both deep branches of the ar­chaeal bush. Or­thologs of tubu­lin have turned up in Ni­trosoar­chaeum, a mem­ber of the novel phy­lum Thau­mar­chaeota, which is an­other an­cient branch (19). Just to con­fuse mat­ters, tubu­lins also oc­cur in the bac­te­r­ial phy­lum Pros­theto­bac­ter. And Cre­nar­chaeota pos­sess a membrane–remodeling sys­tem re­lated to the ESCRT-III sys­tem of eu­kary­otes (13). Taken to­gether, the data sug­gest that the eu­kary­otic lin­eage branched off early in the evo­lu­tion of the Ar­chaea, prior to the ap­pear­ance of the cur­rent lines, and that they re­tain many traces of that com­mon an­ces­try.

Don't look now, but just pos­si­bly a glimpse of the elu­sive host is tak­ing shape: nei­ther a clas­si­cal prim­i­tive phago­cyte nor a stan­dard prokary­ote, but some­thing with fea­tures of both. A com­plex cy­toskele­ton, with the ca­pac­ity to form mem­brane pro­tru­sions, hints at a novel way to make a liv­ing. Like Gas­par Jèkely (10), I like to imag­ine that the pri­mor­dial mi­cro­bial mats and biofilms of­fered a niche to prim­i­tive scav­engers and preda­tors that felt no need to com­pete with the prokary­otic pri­mary pro­duc­ers; in­stead, they ate them. Sometimes—conceivably, just once—the prey evaded di­ges­tion and es­tab­lished res­i­dence. The host con­tributed the ge­netic core, the cy­toskele­ton, AT­Pases, and prob­a­bly much else; the sym­biont of­fered genes and a glo­ri­ous fu­ture un­tram­meled by en­ergy short­ages. Many loose ends re­main to be tucked in: Whence came sig­na­ture genes found only in eu­kary­otes? How does the me­tab­o­lism of eu­kary­otic cells re­late to that of the hy­po­thet­i­cal scav­enger? Why is the lipid com­po­si­tion of eu­kary­otic plasma mem­branes akin to that of Bac­te­ria rather than Ar­chaea? Even so, it may be the case that we are watch­ing the gen­e­sis of the Eu­karya turn from a mys­tery into a puz­zle.

For mi­cro­bi­ol­o­gists pre­oc­cu­pied with prac­ti­cal mat­ters, the beget­ting of the Eu­karya will seem a neb­u­lous sub­ject best con­tem­plated over a beer. But this ar­cane is­sue im­pinges on one of the con­cep­tual foun­da­tions of mi­cro­bi­ol­ogy, namely the tree of life with its three an­ces­tral do­mains (Fig 1A). The nar­ra­tive sketched above chal­lenges that iconic im­age in two ways. First, if the lin­eage of the eu­kary­otic host branched off within the Ar­chaea, is it still ap­pro­pri­ate to con­sider it a sep­a­rate, in­de­pen­dent line? Well, that will de­pend on the pre­cise re­la­tion­ship of the eu­kary­otic an­ces­tor to the last com­mon an­ces­tor of Ar­chaea, a mat­ter un­likely ever to be un­am­bigu­ously re­solved. To me, the key point is that, from its in­cep­tion, the eu­kary­otic branch seems to have op­er­ated on a dis­tinc­tive pat­tern of or­ga­ni­za­tion; if any group­ing rates the des­ig­na­tion of do­main, it's the Eu­karya. The sec­ond, and more se­ri­ous con­cern, turns on the role of the sym­biont. If sym­bionts came late into a pre-formed proto-eu­kary­otic host, to which they made only a mi­nor con­tri­bu­tion, the im­age of the tree re­mains apt. But if, as now ap­pears, they came early and helped shape the very fab­ric of the eu­kary­otic cell, then the Eu­karya are not a pri­mary do­main but a sec­ondary, or de­rived one (Fig. 1B). Thus the most fit­ting im­age to hold in mind is not a tree, but a pointed Gothic arch thrust­ing out of the prokary­otic un­der­brush to­wards a higher plane of life. Viva Eu­karya!

Ref­er­ences

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Franklin M. Harold, De­part­ment of Microbiology,University of Wash­ing­ton, Seat­tle, WA 98195. E‑Mail: frankharold@earthlink.net