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Three out of the seven ribosomal RNA operons in  Escherichia coli  end in dual terminator structures. Between the two terminators of each operon is a short sequence that we report here to be an sRNA gene, transcribed as part of the ribosomal RNA primary transcript by read-through of the first terminator. The sRNA genes ( rrA ,  rrB  and  rrF ) from the three operons ( rrnA ,  rrnB  and  rrnD ) are more than 98% identical, and pull-down experiments show that their transcripts interact with Hfq and CsrA. Deletion of  rrA, B, F , as well as overexpression of  rrB , only modestly affect known CsrA-regulated phenotypes like biofilm formation,  pgaA  translation and  glgC  translation, and the role of the sRNAs  in vivo  may not yet be fully understood. Since RrA, B, F are short-lived and transcribed along with the ribosomal RNA components, their concentration reflect growth-rate regulation at the ribosomal RNA promoters and they could function to fine-tune other growth-phase-dependent processes in the cell. The primary and secondary structure of these small RNAs are conserved among species belonging to different genera of Enterobacteriales.

Three Ribosomal Operons of Escherichia coli Contain Genes Encoding Small RNAs That Interact With Hfq and CsrA in vitro