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The Secondary Structure of Mammalian Mitochondrial 16S rRNA Molecules: Refinements Based on a Comparative Phylogenetic Approach

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Abstract

Eighty six complete 16S ribosomal RNA (rRNA) gene sequences representing every mammalian order (one monotreme, 33 marsupials, 52 placentals) were employed to establish a core secondary structure model for mammalian 16S rRNA. Starting with the Gutell et al. (1993) and De Rijk et al. (1999) models, we used the criteria of potential base-pairing and positional covariance to make refinements in these models for mammalian 16S rRNA molecules. Our results suggest a mammalian secondary structure model with deletions as well as additions to the Gutell et al. (1993) and De Rijk et al. (1999) models for cow. We recognize 53 stems, 41 of which show at least some positional covariance within Mammalia. In addition, we recognize four tertiary interactions. Stems and loops have distinctly different properties, including base composition and relative substitution rates. Accounting for these differences results in improved models of sequence evolution.

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  1. Department of Biology, University of California, Riverside, CA, 92521, USA

    Angela Burk & Mark S. Springer

  2. Labortoire de Paléontologie, Institut des Sciences de l'Evolution, URA 327 CNRS, Unitersité Montpellier II, Place E. Bataillon, case courrier 064, F-34 095, Montpellier, France

    Emmanuel J. P. Douzery

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Burk, A., Douzery, E.J.P. & Springer, M.S. The Secondary Structure of Mammalian Mitochondrial 16S rRNA Molecules: Refinements Based on a Comparative Phylogenetic Approach. Journal of Mammalian Evolution 9, 225–252 (2002). https://doi.org/10.1023/A:1022649516930

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