Nucleotide sequence, secondary structure and evolution of the 5S ribosomal RNA from five bacterial species

Abstract

The nucleotide sequences of the 5S rRNA species of the bacteria Agrobacterium tumefaciens, Alcaligenes faecalis, Pseudomonas cepacia, Aquaspirillum serpens and Acinetobacter calcoaceticus were determined. The sequences fit in a generally accepted model for 5S RNA secondary structure. A closer comparative examination of these and other bacterial 5S RNA primary structures reveals the potential of additional base pairing and of multiple equilibria between a set of slightly different alternative secondary structures in 1 area of the molecule. The phylogenetic position of the examined bacteria is derived from a 5S RNA sequence alignment by a clustering method and compared with the position derived on the basis of 16S rRNA oligonucleotide catalogs.