Detection of pur operon-attenuated mRNA and accumulated degradation intermediates in Bacillus subtilis.

Transcription of the Bacillus subtilis pur operon is regulated independently by adenine and guanine nucleotides (Ebbole, D. J., and Zalkin, H. (1987) J. Biol. Chem. 262, 8274-8287). Guanine nucleotides regulate transcription by a termination-antitermination mechanism in a 242-nucleotide, 5'-untranslated mRNA leader region. We have identified an apparently intact, terminated transcript of approximately 200 nucleotides in length, having a half-life of about 0.7 min. The terminated transcript is degraded in a series of discrete steps resulting in the accumulation of stable intermediates in vivo. We have used Northern blot analysis, primer extension, and nuclease S1 mapping to align the degradation intermediates with the nucleotide sequence and assign secondary structures that may contribute to the stability of the intermediates. Degradation is initiated by endonucleolytic cleavage of the approximately 200-nucleotide terminated transcript generating approximately 93- and approximately 97-nucleotide 5' and 3' moieties, respectively. The approximately 93-nucleotide 5' and approximately 97-nucleotide 3' intermediates are further degraded to approximately 88 and approximately 58 nucleotides, respectively. The 5'-end of pur operon mRNA and the attenuated transcript are degraded by different pathways.