All living beings are composed of cells and are unambiguously classifiable into one of two categories: prokaryote (bacteria) or eukaryote (nucleated organisms). Here we outline the origin of the nucleus, the membrane-bounded organelle that defines eukaryotes. The common ancestor of all eukaryotes by genome fusion of two or more different prokaryotes became “chimeras” via symbiogenesis (1). Long term physical association between metabolically dependent consortia bacteria led, by genetic fusion, to this chimera. The chimera originated when an archaebacterium (a thermoacidophil) and a motile eubacterium emerged under selective pressure: oxygen threat and scarcity both of carbon compounds and electron acceptors. The nucleus evolved in the chimera. The earliest descendant of this momentous merger, if alive today, would be recognized as an amitochondriate protist. An advantage of our model includes its simultaneous consistency in the evolutionary scenario across fields of science: cell biology, developmental biology, ecology, genetics, microbiology, molecular evolution, paleontology, protistology. Environmentally plausible habitats and modern taxa are easily comprehensible as legacies of the fusion event. The scheme that generates predictions demonstrable by molecular biology, especially motile protein sequence comparisons (2), provides insight into the structure, physiology, and classification of microorganisms.
Our analysis requires the two- (Bacteria/Eukarya) not the three- (Archaea/Eubacteria/Eukarya) domain system (3). The prokaryote vs. eukaryote that replaced the animal vs. plant dichotomy so far has resisted every challenge. Microbiologist's molecular biology-based threat to the prokaryote vs. eukaryote evolutionary distinction seems idle (4). In a history of contradictory classifications of microorganisms since 1820, Scamardella (5) noted that Woese's entirely nonmorphological system ignores symbioses. But bacterial consortia and protist endosymbioses irreducibly underlie evolutionary transitions from prokaryotes to eukaryotes. Although some prokaryotes [certain Gram-positive bacteria (6)] are intermediate between eubacteria and archaebacteria, no organisms intermediate between prokaryotes and eukaryotes exist. These facts render the 16S rRNA and other nonmorphological taxonomies of Woese and others inadequate. Only all-inclusive taxonomy, based on the work of thousands of investigators over more than 200 years on live organisms (7), suffices for detailed evolutionary reconstruction (4).
When Woese (8) insists “there are actually three, not two, primary phylogenetic groupings of organisms on this planet” and claims that they, the “Archaebacteria” (or, in his term that tries to deny their bacterial nature, the “Archaea”) and the “Eubacteria” are “each no more like the other than they are like eukaryotes,” he denies intracellular motility, including that of the mitotic nucleus. He minimizes these and other cell biological data, sexual life histories including cyclical cell fusion, fossil record correlation (9), and protein-based molecular comparisons (10, 11). The tacit, uninformed assumption of Woese and other molecular biologists that all heredity resides in nuclear genes is patently contradicted by embryological, cytological, and cytoplasmic heredity literature (12). The tubulin-actin motility systems of feeding and sexual cell fusion facilitate frequent viable incorporation of heterologous nucleic acid. Many eukaryotes, but no prokaryotes, regularly ingest entire cells, including, of course, their genomes, in a single phagocytotic event. This invalidates any single measure alone, including ribosomal RNA gene sequences, to represent the evolutionary history of a lineage.
As chimeras, eukaryotes that evolved by integration of more than a single prokaryotic genome (6) differ qualitatively from prokaryotes. Because prokaryotes are not directly comparable to symbiotically generated eukaryotes, we must reject Woese's three-domain interpretation. Yet our model greatly appreciates his archaebacterial-eubacterial distinction: the very first anaerobic eukaryotes derived from both of these prokaryotic lineages. The enzymes of protein synthesis in eukaryotes come primarily from archaebacteria whereas in the motility system (microtubules and their organizing centers), many soluble heat-shock and other proteins originated from eubacteria (9). Here we apply Gupta's idea (from protein sequences) (10) to comparative protist data (13) to show how two kinds of prokaryotes made the first chimeric eukaryote. We reconstruct the fusion event that produced the nucleus.