Secondary structure and patterns of evolution among mammalian mitochondrial 12S rRNA molecules. J.Mol.Evol. 43: 357-73

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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Available from: Mark Springer, Oct 02, 2015
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    • "We partitioned the aligned genomes into protein-coding genes, tRNAs, rRNAs, and noncoding fragments (including the origin of replication and the hypervariable region) [10]. We further partitioned the protein-coding genes based on amino acid sequences, into stems and loops data for rRNAs [62], [63] and cloverleaf pattern for tRNAs, which correspond to RNA secondary structures of those genes. Protein-coding genes were aligned manually based on the deduced amino acid sequences. "
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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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    • "RNAsalsa, specifically designed to align ribosomal RNAs, uses preexisting knowledge of RNA structure to simultaneously predict secondary structure in the RNA sequences and to align them based on the secondary structure information. We used secondary structures of Bos taurus as reported in the literature (Springer and Douzery, 1996; Burk and Douzery, 2002; Stocsits et al., 2009) to align the remaining 86 sequences in our dataset. RAF (RNA Alignment and Folding) uses an algorithm for simultaneous alignment and consensus folding of unaligned RNA sequences. "
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