Evolved RNA secondary structure and the rooting of the universal tree of life

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...

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Bibliographic Details
Published in:Journal of molecular evolution 2002-03, Vol.54 (3), p.333-345
Main Author: Caetano Anolles, G
Format: Article
Language:English
Subjects:
Animals
Archaea
Bacteria
Biosynthesis
Eucarya
Evolution, Molecular
Evolutionary biology
Genomics
Humans
Molecular biology
Nucleic Acid Conformation
Nucleic acids
Phylogeny
Proteins
Ribonucleic acid
RNA
RNA, Ribosomal - chemistry
rRNA
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Summary: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.
ISSN:0022-2844
1432-1432
DOI:10.1007/s00239-001-0048-3