Colloquium The chimeric eukaryote: Origin of the nucleus from the karyomastigont in amitochondriate protists Lynn Margulis*, Michael F. Dolan*†, and Ricardo Guerrero‡ *Department of Geosciences, Organismic and Evolutionary Biology Graduate Program, University of Massachusetts, Amherst, MA 01003; and ‡Department of Microbiology, and Special Research Center Complex Systems (Microbiology Group), University of Barcelona, 08028 Barcelona, Spain We present a testable model for the origin of the nucleus, the provides insight into the structure, physiology, and classification membrane-bounded organelle that defines eukaryotes. A chimeric of microorganisms. cell evolved via symbiogenesis by syntrophic merger between an Our analysis requires the two- (Bacteria͞Eukarya) not the three- archaebacterium and a eubacterium. The archaebacterium, a ther- (Archaea͞Eubacteria͞Eukarya) domain system (3). The pro- moacidophil resembling extant Thermoplasma, generated hydro- karyote vs. eukaryote that replaced the animal vs. plant dichotomy gen sulfide to protect the eubacterium, a heterotrophic swimmer so far has resisted every challenge. Microbiologist’s molecular comparable to Spirochaeta or Hollandina that oxidized sulfide to biology-based threat to the prokaryote vs. eukaryote evolutionary sulfur. Selection pressure for speed swimming and oxygen avoid- distinction seems idle (4). In a history of contradictory classifica- ance led to an ancient analogue of the extant cosmopolitan tions of microorganisms since 1820, Scamardella (5) noted that bacterial consortium ‘‘Thiodendron latens.’’ By eubacterial-archae- Woese’s entirely nonmorphological system ignores symbioses. But bacterial genetic integration, the chimera, an amitochondriate bacterial consortia and protist endosymbioses irreducibly underlie heterotroph, evolved. This ‘‘earliest branching protist’’ that formed evolutionary transitions from prokaryotes to eukaryotes. Although by permanent DNA recombination generated the nucleus as a some prokaryotes [certain Gram-positive bacteria (6)] are inter- component of the karyomastigont, an intracellular complex that mediate between eubacteria and archaebacteria, no organisms assured genetic continuity of the former symbionts. The karyo- intermediate between prokaryotes and eukaryotes exist. These mastigont organellar system, common in extant amitochondriate facts render the 16S rRNA and other nonmorphological taxono- protists as well as in presumed mitochondriate ancestors, mini- mies of Woese and others inadequate. Only all-inclusive taxonomy, mally consists of a single nucleus, a single kinetosome and their based on the work of thousands of investigators over more than 200 protein connector. As predecessor of standard mitosis, the karyo- years on live organisms (7), suffices for detailed evolutionary mastigont preceded free (unattached) nuclei. The nucleus evolved reconstruction (4). in karyomastigont ancestors by detachment at least five times When Woese (8) insists ‘‘there are actually three, not two, (archamoebae, calonymphids, chlorophyte green algae, ciliates, primary phylogenetic groupings of organisms on this planet’’ and foraminifera). This specific model of syntrophic chimeric fusion can claims that they, the ‘‘Archaebacteria’’ (or, in his term that tries be proved by sequence comparison of functional domains of to deny their bacterial nature, the ‘‘Archaea’’) and the ‘‘Eubac- motility proteins isolated from candidate taxa. teria’’ are ‘‘each no more like the other than they are like eukaryotes,’’ he denies intracellular motility, including that of Archaeprotists ͉ spirochetes ͉ sulfur syntrophy ͉ the mitotic nucleus. He minimizes these and other cell biological Thiodendron ͉ trichomonad data, sexual life histories including cyclical cell fusion, fossil record correlation (9), and protein-based molecular compari- Two Domains, Not Three sons (10, 11). The tacit, uninformed assumption of Woese and other molecular biologists that all heredity resides in nuclear ll living beings are composed of cells and are unambiguously genes is patently contradicted by embryological, cytological, and Aclassifiable into one of two categories: prokaryote (bacte- cytoplasmic heredity literature (12). The tubulin-actin motility ria) or eukaryote (nucleated organisms). Here we outline the systems of feeding and sexual cell fusion facilitate frequent origin of the nucleus, the membrane-bounded organelle that viable incorporation of heterologous nucleic acid. Many eu- defines eukaryotes. The common ancestor of all eukaryotes by karyotes, but no prokaryotes, regularly ingest entire cells, in- genome fusion of two or more different prokaryotes became cluding, of course, their genomes, in a single phagocytotic event. ‘‘chimeras’’ via symbiogenesis (1). Long term physical associa- This invalidates any single measure alone, including ribosomal tion between metabolically dependent consortia bacteria led, by RNA gene sequences, to represent the evolutionary history of a genetic fusion, to this chimera. The chimera originated when an lineage. archaebacterium (a thermoacidophil) and a motile eubacterium As chimeras, eukaryotes that evolved by integration of more emerged under selective pressure: oxygen threat and scarcity than a single prokaryotic genome (6) differ qualitatively from both of carbon compounds and electron acceptors. The nucleus prokaryotes. Because prokaryotes are not directly comparable to evolved in the chimera. The earliest descendant of this momen- symbiotically generated eukaryotes, we must reject Woese’s tous merger, if alive today, would be recognized as an amito- three-domain interpretation. Yet our model greatly appreciates chondriate protist. An advantage of our model includes its his archaebacterial-eubacterial distinction: the very first anaer- simultaneous consistency in the evolutionary scenario across obic eukaryotes derived from both of these prokaryotic lineages. fields of science: cell biology, developmental biology, ecology, The enzymes of protein synthesis in eukaryotes come primarily genetics, microbiology, molecular evolution, paleontology, pro- tistology. Environmentally plausible habitats and modern taxa This paper was presented at the National Academy of Sciences colloquium ‘‘Variation and are easily comprehensible as legacies of the fusion event. The Evolution in Plants and Microorganisms: Toward a New Synthesis 50 Years After Stebbins,’’ scheme that generates predictions demonstrable by molecular held January 27–29, 2000, at the Arnold and Mabel Beckman Center in Irvine, CA. biology, especially motile protein sequence comparisons (2), †To whom reprint requests should be addressed. E-mail: [email protected]. 6954–6959 ͉ PNAS ͉ June 20, 2000 ͉ vol. 97 ͉ no. 13 Downloaded by guest on September 28, 2021 Fig. 1. Origin of the chimeric eukaryote with karyomastigonts from a motile sulfur-bacteria consortium. from archaebacteria whereas in the motility system (microtu- acceptor. As does its extant descendant, the ancient archaebac- bules and their organizing centers), many soluble heat-shock and terium survived acid-hydrolysis environmental conditions by other proteins originated from eubacteria (9). Here we apply nucleosome-style histone-like protein coating of its DNA (14) Gupta’s idea (from protein sequences) (10) to comparative and actin-like stress-protein synthesis (15). The wall-less archae- protist data (13) to show how two kinds of prokaryotes made the bacterium was remarkably pleiomorphic; it tended into tight COLLOQUIUM first chimeric eukaryote. We reconstruct the fusion event that physical association with globules of elemental sulfur by use of produced the nucleus. its rudimentary cytoskeletal system (16). The second member of the consortium, an obligate anaerobe, required for growth the The Chimera: Archaebacterium͞Eubacterium Merger highly reduced conditions provided by sulfur and sulfate reduc- Study of conserved protein sequences [a far larger data set than tion to hydrogen sulfide. Degradation of carbohydrate (e.g., that used by Woese et al. (3)] led Gupta (10) to conclude “all starch, sugars such as cellobiose) and oxidation of the sulfide to eukaryotic cells, including amitochondriate and aplastidic cells elemental sulfur by the eubacterium generated carbon-rich received major genetic contributions to the nuclear genome from fermentation products and electron acceptors for the archae- both an archaebacterium (very probably of the eocyte, i.e., bacterium. When swimming eubacteria attached to the archae- thermoacidophil group and a Gram-negative bacterium . [t]he bacterium, the likelihood that the consortium efficiently reached ancestral eukaryotic cell never directly descended from archae- its carbon sources was enhanced. This hypothetical consortium, bacteria but instead was a chimera formed by fusion and before the integration to form a chimera (Fig. 1), differs little integration of the genomes of an archaebacerium and a Gram- negative bacterium” (p. 1487). The eubacterium ancestor has yet from the widespread and geochemically important “Thioden- to be identified; Gupta rejects our spirochete hypothesis. In dron” (17, 18). answer to which microbe provided the eubacterial contribution, The ‘‘Thiodendron’’ Stage he claims: “the sequence data ....suggest that the archaebac- teria are polyphyletic and are close relatives of the Gram-positive The ‘‘Thiodendron’’ stage refers to an extant bacterial consor- bacteria” (p. 1485). The archaebacterial sequences, we posit, tium that models our idea of an archaebacteria-eubacteria