1990 Cold Spring Harbor RNA Processing Meeting, Cold Spring Harbor, N.Y.

Phylogenetic analysis and evolution of RNase P RNA in purple eubacteria

James W. Brown, Elizabeth S. Haas, Dirk A. Hunt, Jin-Song Lee and Norman R. Pace
Department of Biology, and Institute for Molecular and Cellular Developmental Biology,
Indiana University, Bloomington, IN 47405

The genes encoding the RNA subunit of ribonuclease P (RNase P RNA) from the a-purple eubacteria Agrobacterium tumefaciens (402nt) and Rhodospirillum rubrum (429nt), the b-purple eubacterium Alcaligenes eutrophus (341nt) and the d-purple eubacterium Desulfovibrio desulfuricans (360nt) have been cloned and sequenced. Taken with the previously sequenced genes for RNase P RNAs from several g-purple, this represents a sampling of each of the phylogenetic branches of purple eubacteria.

These RNase P RNA sequences allow refinement of the phylogenetic model for RNase P RNA secondary structure, which was originally based on the sequences of RNase P RNAs from four species of the genus Bacillus (Gram positive eubacteria) and seven g-purple eubacteria (mostly closely related enterobacteria). The phylogenetic model has been strengthened by covariation of previously invarient nucleotides within helical elements in the structure model. The evidence for all previously identified helices have been strengthened; in some cases these helices have been lengthened by new covariation or shortened by non-covariation of potential base pairings. Previously unobserved secondary and higher-order structural covariations, including conserved non-canonical pairings, are presented.

These additional sequences have also been used to construct a parsimonious model for the evolution of RNase P RNA primary and secondary structure in purple eubacteria and Bacillus, and allows the reconstruction of ancestral RNase P RNAs. Evolutionary change among the RNase P RNAs occurs primarily in discrete structural domains which are peripheral to the highly conserved "core" structure of RNase P RNA. Analysis of evolutionary changes in the group-specific structural elements has been used to identify features useful in the design of improved synthetic "minimal" RNase P RNAs.

Phylogenetic trees based on sequence alignments and signature elements of RNase P RNAs are not in agreement with those derived from 16S rRNA sequences. The differences in branching order seem to result from an unusually high rate of evolution of RNase P RNA sequence and structure in Alcaligenes eutrophus, which is in agreement with the previously observed high "clock-rate" of 16S rRNA in b-purple eubacteria relative to other purple eubacteria.