Figure 5

Aquificales 6S RNAs: predicted pRNA transcription initiation sites, and pRNA-induced structural rearrangements of 6S RNAs. Top: A. aeolicus 6S RNA; this 6S RNA was experimentally verified [85] and the pRNA transcription start site identified by deep sequencing (unpublished results); nucleotides of the central bulge region are marked in blue; during pRNA transcription on 6S RNA as template, the endogenous helix is disrupted, leading to the formation of new base-pairing interactions. Here, a 6S RNA hybrid with a pRNA 13-mer (red) is shown on the right; the proposed rearranged structure of the central 6S RNA region [90] has not yet been proven experimentally. Proposed structures of the central bulge regions and their pRNA-induced rearrangements of the other eight Aquificales 6S RNA candidates: rearranged structures upon duplex formation with putative pRNA 13-mers; the pRNA initiation sites are proposed on the basis of resemblance to A. aeolicus 6S RNA. For more details, see Supplemental Material.