Autoregulation of RNase E synthesis: Predominant impact of a branched RNA stem-loop to which the nuclease binds

Due to its crucial role in proteobacterial RNA processing and degradation, the synthesis of the endonuclease RNase E is tightly controlled by a post-transcriptional autoregulatory mechanism governed by the 5' untranslated region of rne mRNA, the transcript that encodes it. Previous studies have identified one structural component of the rne 5' untranslated region (hp2) that helps to mediate this process in Escherichia coli by binding to RNase E. Here, we show that another component (hp3), a branched stem-loop, makes an even greater contribution to feedback regulation of RNase E synthesis and that the effects of hp2 and hp3 are additive, suggesting independent function. Despite the structural complexity of hp3, a single constituent branch appears to be the principal source of its regulatory activity. This branch also enables hp3 to bind RNase E with high affinity. The secondary structure of this branch, including the presence of two internal loops essential for its impact, is conserved in diverse Enterobacterales species, whereas the sequence of the internal loops is not. We propose that hp2 and hp3 mediate autoregulation by recruiting RNase E to the rne transcript.