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

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 pulldown
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 finetune
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.