Bacterial non-coding RNAs excised from within protein-coding transcripts

Prokaryotic genomes encode a plethora of small non-coding RNAs (ncRNAs) that fine-tune the expression of specific genes. The vast majority of known bacterial ncRNAs are encoded from within intergenic regions, where their expression is controlled by promoter and terminator elements, similarly to protein-coding genes. However, recent studies have shown that functional ncRNAs can also be derived from gene 3' Untranslated Regions (3'UTRs) via an alternative biogenesis pathway, in which the ncRNA segment is separated from the mRNA via RNase cleavage. Here, we report the detection of a large set of decay-generated non-coding RNAs (decRNAs), many of which are completely embedded within protein-coding mRNA regions, rather than in the UTRs. We show that these decRNAs are “carved” out of the mRNA through the action of RNase E, and are predicted to fold into highly stable RNA structures, similar to those of known ncRNAs. A subset of these decRNAs is predicted to interact with Hfq and/or ProQ, which act as ncRNA chaperones, and some decRNAs display evolutionarily conserved sequences and conserved expression patterns between different species. These results suggest mRNA protein-coding regions may harbor a large set of potentially functional small RNAs.