THE MITOCHONDRIAL RIBOSOMAL-RNA GENES OF THE NEMATODES CAENORHABDITIS-ELEGANS AND ASCARIS-SUUM - CONSENSUS SECONDARY-STRUCTURE MODELS AND CONSERVED NUCLEOTIDE SETS FOR PHYLOGENETIC ANALYSIS

The small- and large-subunit mitochondrial ribosomal RNA genes (mt-s-r RNA and mt-1-rRNA) of the nematode worms Caenorhabditis elegans and As caris suum encode the smallest rRNAs so far reported for metazoa. Thes e size reductions correlate with the previously described, smaller, st ructurally anomalous mt-tRNAs of C. elegans and A. suum. Using primer extension analysis, the 5' end nucleotides of the mt-s-rRNA and mt-1-r RNA genes were determined to be adjacent to the 3' end nucleotides of the tRNA(Glu) and tRNA(His) genes, respectively. Detailed, consensus s econdary-structure models were constructed for the mt-s-rRNA genes and the 3' 64% of mt-1-rRNA genes of the two nematodes. The mt-s-rRNA sec ondary-structure model bears a remarkable resemblance to the previousl y defined universal core structure of E. coli 16S rRNA: most of the nu cleotides that have been classified as variable or semiconserved in th e E. coli model appear to have been eliminated from the C. elegans and A. suum sequences. Also, the secondary structure model constructed fo r the 3' 64% of the mt-1-rRNA is similar to the corresponding portion of the previously defined E. coli 23S rRNA core secondary structure. T he proposed C. elegans/A. suum mt-s-rRNA and mt-1-rRNA models include all of the secondary-structure element-forming sequences that in E. co li rRNAs contain nucleotides important for A-site and P-site (but not E-site) interactions with tRNAs. Sets of apparently homologous sequenc es within the mt-s-rRNA and mt-1-rRNA core structures, derived by alig nment of the C. elegans and A. suum mt-rRNAs to the corresponding mt-r RNAs of other eukaryotes, and E. coli rRNAs were used in maximum-likel ihood analyses. The patterns of divergence of metazoan phyla obtained show considerable agreement with the most prevalent metazoan divergenc e patterns derived from more classical, morphological, and development al data.