Mechanism of puf mRNA degradation: the role of an intercistronic stem-loop structure.

The puf photosynthesis operon of Rhodobacter capsulatus encodes two major classes of mRNA: operon-length pufBALMX transcripts and short pufBA messages. The pufBA messages, which end in a large intercistronic stem-loop structure, are long-lived processing products of the puf operon transcripts. Decay of the labile pufLMX segment of the operon-length transcripts begins with non-random endonucleolytic cleavage well downstream of the intercistronic hairpin structure. This hairpin, which is necessary but insufficient for the stability of the RNA segment upstream of it, appears to function as an mRNA decay terminator that protects the upstream pufBA segment from 3' exonucleolytic propagation of the initial degradative event. The comparative stability of the pufBA mRNA segment depends not only on the presence of this stem-loop structure, but also on the relative resistance of the pufBA segment to endonuclease attack.