AUTHOR=Stenum Thomas Søndergaard , Kongstad Mette , Holmqvist Erik , Kallipolitis Birgitte , Svenningsen Sine Lo , Sørensen Michael Askvad 

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

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.625585

DOI=10.3389/fmicb.2021.625585

ISSN=1664-302X

ABSTRACT=<p>Three out of the seven ribosomal RNA operons in <italic>Escherichia coli</italic> 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 (<italic>rrA</italic>, <italic>rrB</italic> and <italic>rrF</italic>) from the three operons (<italic>rrnA</italic>, <italic>rrnB</italic> and <italic>rrnD</italic>) are more than 98% identical, and pull-down experiments show that their transcripts interact with Hfq and CsrA. Deletion of <italic>rrA, B, F</italic>, as well as overexpression of <italic>rrB</italic>, only modestly affect known CsrA-regulated phenotypes like biofilm formation, <italic>pgaA</italic> translation and <italic>glgC</italic> translation, and the role of the sRNAs <italic>in vivo</italic> 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.</p>