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

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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.