COMPARATIVE-ANALYSIS OF RIBONUCLEASE-P RNA USING GENE-SEQUENCES FROM NATURAL MICROBIAL-POPULATIONS REVEALS TERTIARY STRUCTURAL ELEMENTS

PCR amplification of template DNAs extracted from mixed, naturally occ urring microbial populations, using oligonucleotide primers complement ary to highly conserved sequences, was used to obtain a large collecti on of diverse RNase P RNA-encoding genes, An alignment of these sequen ces was used in a comparative analysis of RNase P RNA secondary and te rtiary structure, The new sequences confirm the secondary structure mo del based on sequences from cultivated organisms (with minor alteratio ns in helices P12 and P18), providing additional support for nearly ev ery base pair. Analysis of sequence covariation using the entire RNase P RNA data set reveals elements of tertiary structure in the RNA; the third nucleotides (underlined) of the GNRA tetraloops L14 and L18 are seen to interact with adjacent Watson-Crick base pairs in helix P8, f orming A:G/C or G:A/U base triples. These experiments demonstrate one way in which the enormous diversity of natural microbial populations c an be used to elucidate molecular structure through comparative analys is.