Fig. 8: Determination of the 3’ and 5’ ends of the 16S rRNA.

a DNA sequencing electrophoregrams of the amplified 16S gene from S. solfataricus cells. Regions around the putative 3’-end of the 16S rRNA are boxed. 16S rDNA shows a CCTCA sequence. b Mapping of the 5’-end of the 16S rRNA using reverse transcription (RT). Lanes 1 to 4: DNA sequencing ladder of the amplified 16S gene using the reverse transcription primer. The complementary RNA sequence is shown on the left. Line 5: reverse transcription analysis of the 16S rRNA using the 5’ mapping reverse transcription primer. The arrest is indicated by an arrow. This experiment shows that the 5’-end of the 16S rRNA starts with the 5’-AAUCC sequence. The first base is indicated by a star. This experiment was performed twice (n = 2). c Identification of the 3’-end of the 16S rRNA. The 16S rRNA was first circularized using T4 RNA ligase, RT-PCR amplified (n = 1) and sequenced (n = 2). Left: sequencing of the RT-PCR amplified ligated 16S rRNA fragment. This qualitative experiment identified that the major sequence of the 3’ end is CCUCC. This result is consistent with the rRNA oligonucleotide catalogs that were early published⁸⁶. In parallel, a XhoI-BamHI fragment from the RT-PCR material, containing the 3’ and 5’ regions, was cloned into a pBS plasmid. Thirty-two independent clones were sequenced. The results show heterogeneity in the length of the 16S rRNA, as discussed in the text. Source data are provided as a Source Data file.