Spliceosomal introns in a deep-branching eukaryote: The splice of life

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Abstract
The classification of all living organisms into three major divisions, Archaea (archaebacteria), Bacteria (eubacteria) and Eukarya (eukaryotes), over two decades ago (1) has changed our view of the relationship between nucleated cells (eukaryotes) and those lacking nuclei (archaebacteria and eubacteria). The foundation for this reclassification of living organisms was originally based on molecular phylogenies constructed by using small subunit ribosomal RNAs (rRNAs) (see Fig. 1) and has since been confirmed by analyses of numerous biochemical properties, as well as the entire genome sequence of organisms within each division. Converging molecular comparisons of diverse properties of organisms within and between domains have led to the proposal that the eukaryotic cell is a hybrid arising from a host archaeal cell and eubacterial endosymbionts (2–4). Representative tree depicting the three domains of life, Bacteria, Archaea, and Eukaryotes, with emphasis on the eukaryotic branch. The tree is based on small subunit rRNA sequences originally published by Sogin (32) and was redrawn by Dacks and Doolittle (2). This tree has provided enormous intellectual stimuli upon which numerous theories have been built and tested. Construction of eukaryotic phylogenies is a continuous process being steadily fed and modified by the availability of new data in this era of genomics. As discussed by Nixon et al. (11) in this issue of PNAS, the precise nature of deep-branching, divergent lineages and their relationship to other eukaryotes continues to be challenged and debated. [Reproduced with permission from ref. 2 (Copyright 2001, Elsevier Science).] Eukaryotes are divided into four kingdoms: Animalia, Plantae, Fungi, and Protista. The bulk of research on eukaryotes has been conducted on fungi, animals, and plants, the “crown group” organisms in rRNA trees, whereas relatively little is known about protist biology. Protists were traditionally classified by their morphology into flagellates, ciliates, amoebae, and sporozoa (5). Only …