Springer, M. S. & Douzery, D. Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules. J. Mol. Evol. 43, 357-373

Department of Biology, University of California, Riverside, CA 92521, USA.
Journal of Molecular Evolution (Impact Factor: 1.68). 11/1996; 43(4):357-73. DOI: 10.1007/BF02339010
Source: PubMed


Forty-nine complete 12S ribosomal RNA (rRNA) gene sequences from a diverse assortment of mammals (one monotreme, 11 marsupials, 37 placentals), including 11 new sequences, were employed to establish a "core" secondary structure model for mammalian 12S rRNA. Base-pairing interactions were assessed according to the criteria of potential base-pairing as well as evidence for base-pairing in the form of compensatory mutations. In cases where compensatory evidence was not available among mammalian sequences, we evaluated evidence among other vertebrate 12S rRNAs. Our results suggest a core model for secondary structure in mammalian 12S rRNAs with deletions as well as additions to the Gutell (1994: Nucleic Acids Res. 22) models for Bos and Homo. In all, we recognize 40 stems, 34 of which are supported by at least some compensatory evidence within Mammalia. We also investigated the occurrence and conservation in mammalian 12S rRNAs of nucleotide positions that are known to participate in the decoding site in E. coli. Twenty-four nucleotide positions known to participate in the decoding site in E. coli also occur among mammalian 12S rRNAs and 17 are invariant for the same base as in E. coli. Patterns of nucleotide substitution were assessed based on our secondary structure model. Transitions in loops become saturated by approximately 10-20 million years. Transitions in stems, in turn, show partial saturation at 20 million years but divergence continues to increase beyond 100 million years. Transversions accumulate linearly beyond 100 million years in both stems and loops although the rate of accumulation of transversions is three- to fourfold higher in loops. Presumably, this difference results from constraints to maintain pairing in stems.

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    • "Sequences from each gene were multiply aligned to establish character homology in relation to outgroups . For 12S rRNA , we aligned sequences based on the secondary structural model of Springer and Douzery ( 1996 ) after an initial alignment generated in MUSCLE ( Edgar , 2004 ) . At sites where multiple indels made sequence alignment ambiguous , we discarded a total of 198 base pairs ( bp ) from the initial alignment of 1035 bp ( positions 70 - 93 , 117 - 125 , 219 - 236 , 299 - 302 , 326 - 333 , 384 - 408 , 426 - 437 , 503 - 515 , 711 - 719 , 782 - 804 , and 934 - 986 ) . "
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    • "The stem substitution frequency (SF) was calculated as the ratio between the number of substitutions on the stem of RNAs and the number of substitutions on the loop of RNAs. The published secondary structures for tRNAs (Helm et al., 2000) and rRNAs (Springer and Douzery, 1996) were used to define the stem and loop structures. "
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