Ribosomes inhibit an RNase E cleavage which induces the decay of the rpsO mRNA of Escherichia coli.

The hypothesis generally proposed to explain the stabilizing effect of translation on many bacterial mRNAs is that ribosomes mask endoribonuclease sites which control the mRNA decay rate. We present the first demonstration that ribosomes interfere with a particular RNase E processing event responsible for mRNA decay. These experiments used an rpsO mRNA deleted of the translational operator where ribosomal protein S15 autoregulates its synthesis. We demonstrate that ribosomes inhibit the RNase E cleavage, 10 nucleotides downstream of the rpsO coding sequence, responsible for triggering the exonucleolytic decay of the message mediated by polynucleotide phosphorylase. Early termination codons and insertions which increase the length of ribosome-free mRNA between the UAA termination codon and this RNase E site destabilize the translated mRNA and facilitate RNase E cleavage, suggesting that ribosomes sterically inhibit RNase E access to the processing site. Accordingly, a mutation which reduces the distance between these two sites stabilizes the mRNA. Moreover, an experiment showing that a 10 nucleotide insertion which destabilizes the untranslated mRNA does not affect mRNA stability when it is inserted in the coding sequence of a translated mRNA demonstrates that ribosomes can mask an RNA feature, 10-20 nucleotides upstream of the processing site, which contributes to the RNase E cleavage efficiency.     

RNase E is involved in 5'-end 23S rRNA processing in alpha-Proteobacteria

In Rhodobacter capsulatus and Rhizobium leguminosarum, an internal transcribed spacer consisting of helices 9 and 10 is removed during 23S rRNA processing, which leads to the occurrence of a 5.8S-like rRNA. The particular rRNA maturation steps are not known, with exception of the initial RNase III cleavage in helix 9. We found that GC-rich stem-loop structures of helix 9, which are released by RNase III, are immediately degraded. The degradation of helix 10 is slower and its kinetics differs in both species. Nevertheless, the helix 10 processing mechanism is conserved and includes cleavages by RNase E.     

Cleavage properties of an estrogen-regulated polysomal ribonuclease involved in the destabilization of albumin mRNA.

Previous work from this laboratory [Dompenciel,R.E., Garnepudi,V.R. and Schoenberg,D.R. (1995)J. Biol. Chem.270, 6108-6118] described the purification and properties of an estrogen-regulated endonuclease isolated from Xenopus liver polysomes that is involved in the destabilization of albumin mRNA. The present study mapped cleavages made by this enzyme onto the secondary structure of the portion of albumin mRNA bearing the major cleavage sites. The predominant cleavages occur in the overlapping APyrUGA sequence AUUGACUGA present in a single-stranded loop region, and in AUUGA located within a bulged AU-rich stem. A structural mutation which converted the major loop cleavage site to a hairpin bearing one APyrUGA element eliminated cleavage at the intact site. This confirms that the polysomal RNase is specific for single-stranded RNA. Additional point mutations in the major loop characterized the nucleoside sequence requirements for cleavage. Finally, snake venom exonuclease was used to demonstrate the polysomal RNase generates products with a 3' hydroxyl. Binding of an estrogen-induced protein to a portion of the 3'UTR of vitellogenin mRNA may be involved in its stabilization by estrogen [Dodson,R.E. and Shapiro,D.J. (1994)Mol. Cell. Biol.14, 3130-3138]. The core binding site for this protein bears the sequence APyrUGA, suggesting that stabilization may be accomplished by occlusion of a cleavage site for the polysomal RNase.     

Translational activation by the noncoding RNA DsrA involves alternative RNase III processing in the rpoS 5'-leader

The intricate regulation of the Escherichia coli rpoS gene, which encodes the stationary phase sigma-factor sigmaS, includes translational activation by the noncoding RNA DsrA. We observed that the stability of rpoS mRNA, and concomitantly the concentration of sigmaS, were significantly higher in an RNase III-deficient mutant. As no decay intermediates corresponding to the in vitro mapped RNase III cleavage site in the rpoS leader could be detected in vivo, the initial RNase III cleavage appears to be decisive for the observed rapid inactivation of rpoS mRNA. In contrast, we show that base-pairing of DsrA with the rpoS leader creates an alternative RNase III cleavage site within the rpoS/DsrA duplex. This study provides new insights into regulation by small regulatory RNAs in that the molecular function of DsrA not only facilitates ribosome loading on rpoS mRNA, but additionally involves an alternative processing of the target.     

Determinants in the rpsT mRNAs recognized by the 5′‐sensor domain of RNase E

RNase E plays a central role in processing virtually all classes of cellular RNA in many bacterial species. A characteristic feature of RNase E and its paralogue RNase G, as well as several other unrelated ribonucleases, is their preference for 5′‐monophosphorylated substrates. The basis for this property has been explored in vitro. At limiting substrate, cleavage of the rpsT mRNA by RNase E (residues 1–529) is inefficient, requiring excess enzyme. The rpsT mRNA is cleaved sequentially in a 5′ to 3′ direction, with the initial cleavage(s) at positions 116/117 or 190/191 being largely driven by direct entry, independent of the 5′‐terminus or the 5′‐sensor domain of RNase E. Generation of the 147 nt 3′‐limit product requires sequential cleavages that generate 5′‐monophosphorylated termini on intermediates, and the 5′‐sensor domain of RNase E. These requirements can be bypassed with limiting enzyme by deleting a stem‐loop structure adjacent to the site of the major, most distal cleavage. Alternatively, this specific cleavage can be activated substantially by a 5′‐phosphorylated oligonucleotide annealed 5′ to the cleavage site. This finding suggests that monophosphorylated small RNAs may destabilize their mRNA targets by recruiting the 5‐sensor domain of RNase E ‘in trans’.     

Arginine-rich RNA binding domain and protein scaffold domain of RNase E are important for degradation of RNAI but not for that of the Rep mRNA of the ColE2 plasmid

Expression of the replication initiator protein (Rep) of the ColE2 plasmid is controlled by antisense RNA (RNAI). Therefore alterations in processes and/or rates of degradation of these two RNAs would affect the Rep expression. Here, we have shown that the arginine-rich RNA binding domain (ARRBD) of RNase E is important for the initial endoribonucleolytic cleavage of RNAI but dispensable for the endoribonucleolytic cleavages of the Rep mRNA. We have also shown that the protein scaffold domain of RNase E is important for successive exoribonucleolytic degradation of RNAI, suggesting involvement of RhlB, but dispensable for that of the Rep mRNA. Such differences in the initiation and successive steps of degradation between RNAI and the Rep mRNA might be important in determining their individual degradation efficiencies required for a quick response to the changes in the plasmid copy number.     

Polarity effects in the lactose operon of Escherichia coli

An intergenic RNA segment between lacY and lacA of the lactose operon in Escherichia coli is cleaved by RNase P, an endoribonuclease. The cleavage of the intergenic RNA was ten times less efficient than cleavage of a tRNA precursor in vitro. Fragments of the RNase P cleavage product are detectable in vivo in the wild-type strain but not in a mutant strain at the restrictive temperature. The cleavage product that contains lacA in the wild-type strain was quickly degraded. When this intergenic segment was cloned upstream of a reporter gene, the expression of the reporter gene was also inhibited substantially in wild-type E.coli, but not in a temperature sensitive mutant strain in RNase P at the restrictive temperature. These results support data regarding the natural polarity between lacZ versus lacA, the downstream gene.     

Autoregulation allows Escherichia coli RNase E to adjust continuously its synthesis to that of its substrates

The Escherichia coli endonuclease RNase E plays a key role in rRNA maturation and mRNA decay. In particular, it controls the decay of its own mRNA by cleaving it within the 5'-untranslated region (UTR), thereby autoregulating its synthesis. Here, we report that, when the synthesis of an RNase E substrate is artificially induced to high levels in vivo, both the rne mRNA concentration and RNase E synthesis increase abruptly and then decrease to a steady-state level that remains higher than in the absence of induction. Using rne-lacZ fusions that retain or lack the rne 5'UTR, we show that these variations reflect a transient mRNA stabilization mediated by the rne 5'UTR. Finally, by putting RNase E synthesis under the control of an IPTG-controlled promoter, we show that a similar, rne 5'UTR-mediated mRNA stabilization can result from a shortage of RNase E. We conclude that the burst in substrate synthesis has titrated RNase E, stabilizing the rne mRNA by protecting its 5'UTR. However, this stabilization is self-correcting, because it allows the RNase E pool to expand until its mRNA is destabilized again. Thus, autoregulation allows RNase E to adjust its synthesis to that of its substrates, a behaviour that may be common among autoregulated proteins. Incidentally, this adjustment cannot occur when translation is blocked, and we argue that the global mRNA stabilization observed under these conditions originates in part from this defect.