Evolved RNA Secondary Structure and the Rooting of the Universal Tree of Life |
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Authors: | Gustavo Caetano-Anollés |
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Institution: | (1) Laboratory of Molecular Ecology and Evolution and Division of Molecular Biology, Department of Biology, University of Oslo, N-0316 Oslo, Norway, NO |
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Abstract: | The origin and diversification of RNA secondary structure were traced using cladistic methods. Structural components were
coded as polarized and ordered multi-state characters, following a model of character state transformation outlined by considerations
in statistical mechanics. Several classes of functional RNA were analyzed, including ribosomal RNA (rRNA). Considerable phylogenetic
signal was present in their secondary structure. The intrinsically rooted phylogenies reconstructed from evolved RNA structure
depicted those derived from nucleic acid sequence at all taxonomical levels, and grouped organisms in concordance with traditional
classification, especially in the archaeal and eukaryal domains. Natural selection appears therefore to operate early in the
information flow that originates in sequence and ends in an adapted phenotype. When examining the hierarchical classification
of the living world, phylogenetic analysis of secondary structure of the small and large rRNA subunits reconstructed a universal
tree of life that branched in three monophyletic groups corresponding to Eucarya, Archaea, and Bacteria, and was rooted in
the eukaryotic branch. Ribosomal characters involved in the translational cycle could be easily traced and showed that transfer
RNA (tRNA) binding domains in the large rRNA subunit evolved concurrently with the rest of the rRNA molecule. Results suggest
it is equally parsimonious to consider that ancestral unicellular eukaryotes or prokaryotes gave rise to all extant life forms
and provide a rare insight into the early evolution of nucleic acid and protein biosynthesis.
Received: 13 September 2000 / Accepted: 27 August 2001 |
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Keywords: | : Cladistic analysis — Molecular evolution — Ribosomal RNA — Secondary structure — Universal tree |
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