Figure 12.

Model for Cp mRNA degradation and generation of small RNAs. (A) Transcription occurs on both strands of a gene locus and generates abundant mRNA (red) and rare antisense transcripts (blue). M factors stabilize the mRNA and T factors activate its translation. After translation, the mRNA can be delivered to degradation Pathway 1, starting with endoribonucleolytic cleavage followed by exoribonucleolytic degradation. Transcripts in excess, namely mRNAs not bound by an M factor or not activated for translation, are mostly directed toward Pathway 1, but they can also base-pair with antisense RNA: the generated dsRNA is substrate for a dsRNA endonuclease (Pathway 2). A block in translation (T factor mutant, Linc or CAP) will exacerbate Pathway 2. In addition, a block in translation with CAP induces the degradation of the mRNA engaged with ribosomes through endoribonucleolytic cleavage between the stalled ribosomes. (B) By-products of RNA degradation comprise mononucleotides (not shown), M factor footprints, ribosome-protected fragments and s-sRNA (derived from Pathways 1 and 3) as well as as-sRNAs derived from Pathway 2.