The Seed Region of a Small RNA Drives the Controlled Destruction of the Target mRNA by the Endoribonuclease RNase E

Abstract

SummaryNumerous small non-coding RNAs (sRNAs) in bacteria modulate rates of translation initiation and degradation of target mRNAs, which they recognize through base-pairing facilitated by the RNA chaperone Hfq. Recent evidence indicates that the ternary complex of Hfq, sRNA and mRNA guides endoribonuclease RNase E to initiate turnover of both the RNAs. We show that a sRNA not only guides RNase E to a defined site in a target RNA, but also allosterically activates the enzyme by presenting a monophosphate group at the 5′-end of the cognate-pairing “seed.” Moreover, in the absence of the target the 5′-monophosphate makes the sRNA seed region vulnerable to an attack by RNase E against which Hfq confers no protection. These results suggest that the chemical signature and pairing status of the sRNA seed region may help to both ‘proofread’ recognition and activate mRNA cleavage, as part of a dynamic process involving cooperation of RNA, Hfq and RNase E.

Hfq binding changes the structure ofEscherichia colismall noncoding RNAs OxyS and RprA, which are involved in the riboregulation ofrpoS

“…We propose that the OxyS structural changes induced by Hfq create a more preferable RNase E cleavage site, such that degradation of OxyS is enhanced. Recent studies involving MicC, an sRNA that pairs to its mRNA target in the coding region and functions in its down-regulation, indicate that the role of processed MicC (containing a 5 ′ monophosphate) is to guide and activate RNase E to cleave its paired target mRNA leading to mRNA signal removal (Bandyra et al 2012). However, if processed MicC fails to pair to its target mRNA, MicC enters a discard pathway in which it is rapidly degraded by RNase E in the presence of Hfq (Bandyra et al 2012).…”

“…RNase E is known to preferentially cleave 5 ′ monophosphorylated RNA substrates (Mackie 1998), and recent studies have suggested that processing to form 5 ′ monophosphorylated RNAs, potentially via the action of RppH, a pyrophosphohydrolase (Deana et al 2008), may be important for an RNase E-dependent sRNA degradation pathway (Bandyra et al 2012). Consequently, RprA and OxyS were tested in 5 ′ monophosphorylated form.…”

“…However, the binding of RNA to Hfq can also increase its susceptibility to cleavage in some cases. This is caused either by Hfq changing the structure of the RNA, leading to the exposure of novel RNase cleavage sites (Zhang et al 2002), or by targeting specific mRNAs for degradation through the formation of specialized ribonucleoprotein complexes, comprising Hfq, RNase E, and an sRNA (Morita et al 2005;Bandyra et al 2012). This complex is believed to assemble on the C-terminal region (CTR) of RNase E (amino acids 530-1061) and acts to specifically guide RNase E on to the target mRNA for endonucleolytic degradation.…”

Hfq assists small RNAs in binding to the coding sequence of ompD mRNA and in rearranging its structure

“…The coding sequence of Salmonella ompD mRNA contains the binding sites of four sRNAs, which are RybB , SdsR (Frohlich et al 2012), InvR , and MicC (Pfeiffer et al 2009). Among them RybB sRNA represses the initiation of translation , while MicC induces the accelerated decay of ompD mRNA, which is dependent on RNase E (Pfeiffer et al 2009;Bandyra et al 2012). The coimmunoprecipitation studies showed that ompD mRNA was bound by Hfq (Sittka et al 2008).…”

“…SdsR anneals to ompD mRNA outside of the footprint of the initiating ribosome and is expected to affect mRNA decay rather than translation initiation (Frohlich et al 2012). In contrast, the mode of action of MicC was proposed to involve the recruitment of RNase E to its binding site in mRNA leading to the accelerated decay of ompD mRNA (Pfeiffer et al 2009;Bandyra et al 2012). The fact that Hfq facilitates the annealing of sRNAs acting differently on translation (Table 2; Fig.…”