Variation in secondary structure of the 16S rRNA molecule in cyanobacteria with implications for phylogenetic analysis.

Abstract

The analysis of the phylogenetic signal in the sequence of the 16S rRNA gene in cyanobacteria and bacteria has been primarily limited to use of unweighted primary sequence in various cladistic analyses. Such analyses ignore the significance of secondary structure in the 16S rRNA molecule. Structure of this molecule is directly tied to its function, and consequently changes in primary sequence that lead to changes in the secondary structure theoretically have greater evolutionary significance than those changes that do not lead to structural changes. Very little analysis of the impact of primary sequence data on the secondary structure of the small subunit rRNA molecule in cyanobacteria has been reported. Herein is reported a secondary structure model of the full 16S rRNA sequence for Nostoc commune Vaucher ex Bornet et Flahault. We also assess the variability in secondary structure of six variable helices in 180 OTUs of cyanobacteria. Variations were minor in most instances, and the observed motifs were not only similar among these cyanobacteria but also were similar to Escherichia coli, a well-studied, representative non-photosynthetic bacterium. Helix 17 was the most variable helix in terms of structure and length of primary sequence. In order to maintain the motifs, we assumed the presence of non-canonical base pairings in the helices. Phylogenies using primary sequence data alone and using primary sequence data in conjunction with coding for secondary structure were very similar, although secondary structural considerations produced trees that more closely reflected the current ultrastructure-based modern taxonomy in the group.