Figure 6

Sequence alignments and secondary structure predictions of the 8 Yfr2-type ncRNAs identify conserved structure and sequence motifs. A. Secondary structure predictions of the three experimentally confirmed ncRNAs Yfr2a, Yfr2b and Yfr2c from Synechocystis 6803. They share a 12 nt central loop on a long helical stem that is interrupted by at least one bulge at position -4 with regard to this loop (red arrows). Moreover, the first 8–13 nt are predicted to be single-stranded. B. Alignments of all eight predicted Yfr2-type DNA sequences reveal two extremely conserved nucleotide stretches: the short unpaired region at the 5' end as well as the predicted centrally located loop element (labelled by horizontal black arrows). In contrast, the region between these two elements is not conserved in sequence or in its length. The single nucleotide breaking the stem at position -4 with regard to the loop is indicated by a red arrow. Note that the 3' end of the transcribed region has not been mapped. Those sequence stretches resembling "GGA" and "ANGGA" motifs are labelled by a set of black arrows. The non-Synechocystis 6803 sequences are one from Thermosynechococcus (Thermo_Yfr2), two from Microcystis (Micro_Yfr2a and Micro_Yfr2b) and two from Synechococcus 6301 (6301_Yfr2a and 6301_Yfr2b).