Figure 5.

YbeY and RNase R are involved in generation and removal of accumulating fragments. (A) Schematic of 16S rRNA and DNA oligonucleotide probes used for Northern blot analysis in (B) and (C). For the sequences of the indicated probes see Supplementary Table S2. (B) Northern blot analysis of 16S rRNA fragments found in total RNA of hibernation factor mutants and RNase mutants after five days of starvation. The schematics on the right show detected fragments. Grey bars indicate fragments common to both WT and ΔHF, red bars indicate fragments only present in ΔHF. Pink bars indicate overhang in fragments I* and V* of Δrnr and ΔybeY mutants. For additional probes and magnified selected areas in the range of fragment I and fragment V see Supplementary Figure S9. (C) As described in (B). RNA was resolved on 6% urea–PAGE gels for detection of RNA in a lower size range. The schematic on the right shows fragments VI and VII mapped by urea–PAGE and Northern blot analysis. For additional probes see Supplementary Figure S9.