Metastable Folding of Bacillus subtilis glmS Ribozyme Modulates Turnover by RNase J1

Rapid turnover of glmS mRNA in Bacillus subtilis by 5'-3' exoribonuclease RNase J is essential for feedback regulation of glucosamine-6-phosphate (GlcN6P) synthase expression, upon self-cleavage of a GlcN6P-activated ribozyme in the glmS 5' UTR. We used biochemical assays and single molecule fluorescence microscopy to show that initiation of RNase J decay is inefficient and requires approximately 15 5' unpaired nucleotides to form a processive exonuclease complex that is insensitive to downstream RNA structure. When stably folded, the cleaved glmS ribozyme blocks RNase J initiation. However, co-transcriptional ribozyme cleavage and physiological Mg²⁺ levels increase decay by weakening the ribozyme structure. At 22 °C, the processive velocity of RNase J, 23 ± 8 nt/s, is equal to or faster than transcription, indicating that RNase J has the potential to catch elongating polymerases. The results show how the folding stability of 5' mRNA structure contributes to RNase J recognition and the control of mRNA half-life.