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The Eocyte Hypothesis and the Origin of Eukaryotic Cells

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The Eocyte Hypothesis and the Origin of Eukaryotic Cells COMMENTARY The eocyte hypothesis and the origin of eukaryotic cells John M. Archibald1 The Canadian Institute for Advanced Research, Program in Integrated Microbial Biodiversity, Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, Halifax, NS, Canada B3H 1X5 n the June 1984 issue of PNAS, field of microbial systematics: if enough other main archaebacterial line, the eur- James Lake and colleagues (1) genomes from diverse organisms could yarchaeotes (e.g., refs. 2 and 4). Simi- published a provocative article in be sequenced and compared, definitive larly, although analyses of anciently di- which they proposed that eu- answers to questions about evolutionary verged paralogs such as genes encoding Ikaryotes (animals, fungi, plants, and translation elongation factors often [but relationships within and between eubac- protists) evolved from a specific group teria, archaebacteria, and eukaryotes not always (16)] place the root of the of thermophilic prokaryotes, the ‘‘eo- would surely emerge. More specifically, tree of life on the branch leading to eu- cyte’’ archaebacteria (1). Few questions it should be possible to discern how eu- bacteria, they are equivocal as to capture the imagination of biologists like karyotes evolved from prokaryotes (if whether archaebacteria are monophy- the origin of eukaryotic (nucleus-con- indeed that is what happened), and per- letic or whether crenarchaeotes are ad- taining) cells such as our own, and as haps even who among modern-day pro- jacent to eukaryotes (e.g., refs. 17 and additional support accumulated (e.g., karyotic lineages is our closest ancestor. 18). A striking 11-aa insertion in the refs. 2–4) Lake’s eocyte hypothesis gar- Unfortunately, with the sequences of elongation factor 1␣ (EF-1␣) protein nered considerable attention. The idea hundreds of eubacterial, archaebacterial, identified by Rivera and Lake (3) sup- that eukaryotes could have arisen from and eukaryotic genomes has come the ports the eocyte tree, as does the phy- within an already diversified archaebac- realization that the number of univer- logeny of EF-1␣ itself (e.g., refs. 3 and terial lineage was eventually overshad- sally distributed genes suitable for global 17). owed by Woese’s (5) ‘‘three-domains’’ phylogenetic analysis is frustratingly view of life in which archaebacteria (in- New Support for an Old Idea cluding eocytes) represent a natural Cox et al. (6) perform a critical exami- (i.e., monophyletic) group to the exclu- Cox et al. revisit nation of the evidence for and against sion of eukaryotes and eubacteria (5). the eocyte hypothesis and the 3-domains In this issue of PNAS, Cox et al. (6) re- the possibility of an tree: they revisit the phylogeny of large visit the possibility of an archaebacterial subunit (LSU) and small subunit (SSU) origin for eukaryotes by using expanded archaebacterial origin rRNA and carry out a comprehensive molecular sequence datasets and ultra- analysis of a set of 51 genes/proteins modern phylogenetic approaches. Their for eukaryotes. that includes components of the core analyses are a model of rigor and rekin- replication, transcription, and translation dle interesting and important ideas machinery, the so-called ‘‘informational’’ about the prokaryotic antecedents of small (10). Lateral (or horizontal) gene genes (19). Using sophisticated method- eukaryotic cells. transfer has shown itself to be a perva- ologies that accommodate among-site Evolving Views on the Tree of Life sive force in the evolution of both pro- compositional heterogeneity in DNA karyotic and eukaryotic genomes, and and protein sequences (20) and lineage- Next to life itself, the origin of complex even if a ‘‘core’’ set of genes can be specific compositional changes over time cells is one of the most fundamental, identified (and there is much debate on (21), Cox et al. show that a combined and intractable, problems in evolution- this issue), how confident are we that 40-taxon LSU–SSU rRNA dataset pro- ary biology. Progress in this area relies heavily on an understanding of the rela- the phylogenetic signal in these genes duces topologies consistent with the eo- tionships between present-day organ- reflects the vertical history of cells? cyte tree, not the 3-domains tree. Thir- isms, yet despite tremendous advances How meaningful are sequence align- ty-nine of the 51 core proteins analyzed over the last half-century scientists re- ment-independent, gene content-based were found to be heterogeneous in main firmly divided on how to best clas- approaches to resolving the ‘‘tree of amino acid composition, and remark- sify cellular life. Many adhere to the life’’ (11)? To what extent is a ‘‘net of ably, only a single protein (the largest textbook concept of 2 basic types of life’’ a more accurate and useful meta- subunit of RNA polymerase I) gener- cells, prokaryotes and eukaryotes, as phor for describing the full spectrum of ated a statistically robust topology in championed by Stanier and van Niel (7). life on Earth (10, 12–14)? which archaebacteria were monophy- Others posit that at its deepest level life These vexing questions aside, it is im- letic, i.e., crenarchaeotes and eur- is not a dichotomy but a trichotomy portant to consider what analyses of yarchaeotes were each other’s closest comprised of cells belonging to the do- universally distributed genes have, and relatives. The remaining trees provided mains Bacteria, Archaea, and Eukarya, have not, revealed about the relation- no strong evidence for or against either each monophyletic and sufficiently dis- ships between prokaryotes and eu- hypothesis, although of the 35 trees in tinct from one another to warrant equal karyotes. The advent of rRNA gene se- which eukaryotes emerge from within a status (5, 8). The conceptual and practi- quencing led to a revolution in paraphyletic archaebacteria, 8 show the cal challenges associated with establish- microbiology with the discovery of the eocyte topology (6). Consistent with the ing a genealogy-based classification third domain of life, the archaebacteria scheme for microbes have been fiercely (15), but rRNA phylogenies do not in debated for decades (see ref. 9 for re- and of themselves unambiguously sup- Author contributions: J.M.A. wrote the paper. cent review), and the literature is rich in port the monophyly of the group. Some The author declares no conflict of interest. philosophy and rhetoric. analyses in fact place the crenarchaeotes See companion article on page 20356. The genomics revolution of the 1990s [Lake’s eocytes (1)] as the sister group 1E-mail: [email protected]. brought tremendous optimism to the of eukaryotes to the exclusion of the © 2008 by The National Academy of Sciences of the USA www.pnas.org͞cgi͞doi͞10.1073͞pnas.0811118106 PNAS ͉ December 23, 2008 ͉ vol. 105 ͉ no. 51 ͉ 20049–20050 results of Yutin et al. (22), it would ap- the thorn in the side of the eocyte hy- archaeotes relative to euryarchaeotes. pear that individual proteins analyzed in pothesis has always been how to ratio- Indeed, the recent discovery of a novel isolation do not paint a consistent pic- nalize crenarchaeote–eukaryote mono- cell division machinery in diverse cren- ture as to whether the 3-domains tree phyly with the apparent unity of archaeal genera, unrelated to the FtsZ- should be favored over the eocyte tree archaebacteria from the perspective of based system found in euryarchaeotes or vice versa. molecular and cell biology. One of the and with proteins homologous to com- In search of increased resolution, Cox most commonly raised objections is the ponents of the eukaryote-specific endo- et al. (6) performed a battery of addi- fact that archaebacteria possess glycerol- somal protein sorting apparatus (25, 26), tional phylogenetic analyses on a concat- ether membrane lipids, unlike the glyc- raises the possibility that a variety of enated set of 45 proteins culled from erol-ester lipids found in most eubacte- molecular phylogeny-independent char- the original 51-protein dataset by elimi- ria and eukaryotes. If, as the eocyte acters will eventually be brought to bear nating alignments containing multiple hypothesis predicts, the eukaryotic on the validity of the eocyte hypothesis. eukaryotic paralogs. Using this su- nucleocytoplasm evolved from within The extent to which a small fraction permatrix of 5,521 amino acid sites, tra- archaebacteria, eukaryotes would have of the genomes of living organisms can ditional methods such as maximum par- had to replace their ancestral lipid bio- be used to trace the history of cellular simony resulted in the 3-domains synthesis pathway with a eubacterial- lineages dating back Ͼ1 billion years topology, but a strongly-supported eo- type system. At first glance this might will no doubt continue to be debated for cyte tree was obtained when maximum- seem problematic but it is not so diffi- years to come. Regardless, an important likelihood and Bayesian analyses were cult to imagine given that the ‘‘opera- message to be taken from the analysis of performed, even under a ‘‘composition tional’’ genes of eukaryotes are primar- Cox et al. (6) is just how sensitive the homogeneous’’ model. Use of a reduced ily eubacterial in origin, not results of molecular phylogenies involv- amino acid alphabet to minimize the archaebacterial (23). ing anciently diverged sequences can be impact of saturation and/or composi- Conversely, comparative genomic to model misspecification and composi- tional heterogeneity resulted in a robust studies have revealed that most ‘‘infor- tional heterogeneity. Beyond serving as crenarchaeote–eukaryote relationship. mational’’ genes in archaebacteria (e.g., a general impetus for reexamination of In sum, their analyses ‘‘. provide sup- those involved in DNA replication, tran- any number of tough phylogenetic prob- port for the eocyte tree, rather than the scription, and translation) are related to lems, the results of Cox et al. serve to 3-domains tree’’ (6). eukaryotic homologs (23, 24).
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