Decay-Initiating Endoribonucleolytic Cleavage by RNase Y Is Kept under Tight Control via Sequence Preference and Sub-cellular Localisation
Fig 3
T-box riboswitches cleaved by RNase Y.
(A) Layout of the valS T-box, indicating Transcription Start Site (TSS), RNase Y cleavage site (Y-cleavage), the highly conserved T-box motif that binds to the 3' CCA of uncharged tRNAs (Anti-CCA), and the predicted T-box riboswitch transcriptional terminator (TB-Term.). The thick line indicate the terminated T-box RNA, and the dotted thin line indicate the full-length transcript. The approximate extent of the fragment that appears in the J1AGA mutant is shown with a thin line. The probe used for the Northern blot in panel B, is indicated with a thick grey bar. (B) Northern blot showing the terminated glyS T-box riboswitch (TB). A fragment downstream of the RNase Y cleavage site accumulates in the RNase J mutant (Y). Additionally, a sub-fragment of about 125 nt is detectable in the ΔY and Y367AA strains (asterisk). Measured sizes of the detected fragments are indicated to the right. Relative intensities are indicated above each band. Loading was normalised to 5S rRNA (shown separately underneath), and the intensity of the band corresponding to the full-length T-box in WT lane set to 1. (C and D) The leuS T-box, with indications like panel A and B. (E and F). The serS T-box, with indications like panel A and B. (G and H) The glyS T-box, with indications like panel A and B.