Phylogenetic comparative analysis of RNA secondary structure

Comparative analyses have been instrumental in the elucidation of the structures of ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), class I and class II introns, and small nuclear RNAs (snRNAs). This chapter describes the application of phylogenetic comparisons to the evaluation of RNA secondary structure, using as an example the catalytic, RNA moiety of ribonuclease P (RNase P), a ribonucleoprotein, tRNA-processing endonuclease. It illustrates the sequences used for the analysis, which show the inferred secondary structures for the RNase P RNAs of Bacillus subtilis and Escherichia coli. The rRNAs are conservative molecules; homologous sequences are identifiable in the rRNAs of all organisms. These homologous sequences can be used to quantify evolutionary distances between organisms and hence, to identify appropriate organisms for a comparative structure analysis of another RNA.