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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.

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We had previously demonstrated that expression of the cross-reactive idiotypes (CRI) in the phenyltrimethylammonium (TMA) system depends on the presence of a second-order T helper (Th2) cell. Furthermore, we showed that this cell type can be replaced by an idiotype-specific helper factor derived from either a 24-hr concanavalin A supernatant (Con A) or the T cell hybridoma LOP 1.4. This factor, regardless of its source, is idiotype-specific, I-J+, and promotes in vitro expression of the cross-reactive phenyltrimethylammonium idiotype (CRI+-TMA) found on anti-trinitrophenyl antibodies. Because the expression of this idiotype in antigen-primed immune sera is linked to the Ig-1e heavy chain locus, experiments were conducted to test whether the production of this factor was also linked to the same locus. Of the strains tested, only splenocytes derived from the Ig-1e mice, irrespective of their background genetics, produced the factor upon Con A stimulation. Furthermore, the function of the factor is not major histocompatibility complex (MHC)-restricted because Con A supernatants derived from the C57.Ige (H-2b, Ig-1e), NZB (H-2d, Ig-1e), and A.SW (H-2s, Ig-1e) strains promoted CRI+ trinitrophenyl plaque-forming cells in A/J (H-2a, Ig-1e) cultures. Further experiments were carried out to determine if the idiotype-specific factor could promote CRI+ TNP plaque-forming cells in non-Ig-1e strains. To this end, A/J Con A and LOP 1.4-derived supernatants were added to primed C57Bl/6 (H-2b, Ig-1b) and DBA/2 (H-2d, Ig-1c) splenic cultures, both of which do not express serum CRI-TMA or produce the idiotype-enhancing factor. The cultures from either strain in the presence of the factor produced CRI+-TMA trinitrophenyl plaque-forming cells of comparable numbers to the A/J prototype strain. The results suggest an important regulatory role for this factor in allotype-linked expression of dominant idiotypes.

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