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EMBO J. Aug 17, 1998; 17(16): 4790–4797.
PMCID: PMC1170808

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

Abstract

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.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Arraiano CM, Yancey SD, Kushner SR. Stabilization of discrete mRNA breakdown products in ams pnp rnb multiple mutants of Escherichia coli K-12. J Bacteriol. 1988 Oct;170(10):4625–4633. [PMC free article] [PubMed]
  • Baumeister R, Flache P, Melefors O, von Gabain A, Hillen W. Lack of a 5' non-coding region in Tn1721 encoded tetR mRNA is associated with a low efficiency of translation and a short half-life in Escherichia coli. Nucleic Acids Res. 1991 Sep 11;19(17):4595–4600. [PMC free article] [PubMed]
  • Bouvet P, Belasco JG. Control of RNase E-mediated RNA degradation by 5'-terminal base pairing in E. coli. Nature. 1992 Dec 3;360(6403):488–491. [PubMed]
  • Braun F, Hajnsdorf E, Régnier P. Polynucleotide phosphorylase is required for the rapid degradation of the RNase E-processed rpsO mRNA of Escherichia coli devoid of its 3' hairpin. Mol Microbiol. 1996 Mar;19(5):997–1005. [PubMed]
  • Carpousis AJ, Van Houwe G, Ehretsmann C, Krisch HM. Copurification of E. coli RNAase E and PNPase: evidence for a specific association between two enzymes important in RNA processing and degradation. Cell. 1994 Mar 11;76(5):889–900. [PubMed]
  • Cohen SN, McDowall KJ. RNase E: still a wonderfully mysterious enzyme. Mol Microbiol. 1997 Mar;23(6):1099–1106. [PubMed]
  • Cole JR, Nomura M. Changes in the half-life of ribosomal protein messenger RNA caused by translational repression. J Mol Biol. 1986 Apr 5;188(3):383–392. [PubMed]
  • Dotto GP, Enea V, Zinder ND. Functional analysis of bacteriophage f1 intergenic region. Virology. 1981 Oct 30;114(2):463–473. [PubMed]
  • Emory SA, Bouvet P, Belasco JG. A 5'-terminal stem-loop structure can stabilize mRNA in Escherichia coli. Genes Dev. 1992 Jan;6(1):135–148. [PubMed]
  • Hajnsdorf E, Steier O, Coscoy L, Teysset L, Régnier P. Roles of RNase E, RNase II and PNPase in the degradation of the rpsO transcripts of Escherichia coli: stabilizing function of RNase II and evidence for efficient degradation in an ams pnp rnb mutant. EMBO J. 1994 Jul 15;13(14):3368–3377. [PMC free article] [PubMed]
  • Hajnsdorf E, Braun F, Haugel-Nielsen J, Régnier P. Polyadenylylation destabilizes the rpsO mRNA of Escherichia coli. Proc Natl Acad Sci U S A. 1995 Apr 25;92(9):3973–3977. [PMC free article] [PubMed]
  • Hajnsdorf E, Braun F, Haugel-Nielsen J, Le Derout J, Régnier P. Multiple degradation pathways of the rpsO mRNA of Escherichia coli. RNase E interacts with the 5' and 3' extremities of the primary transcript. Biochimie. 1996;78(6):416–424. [PubMed]
  • Hartz D, McPheeters DS, Green L, Gold L. Detection of Escherichia coli ribosome binding at translation initiation sites in the absence of tRNA. J Mol Biol. 1991 Mar 5;218(1):99–105. [PubMed]
  • Haugel-Nielsen J, Hajnsdorf E, Regnier P. The rpsO mRNA of Escherichia coli is polyadenylated at multiple sites resulting from endonucleolytic processing and exonucleolytic degradation. EMBO J. 1996 Jun 17;15(12):3144–3152. [PMC free article] [PubMed]
  • Huang H, Liao J, Cohen SN. Poly(A)- and poly(U)-specific RNA 3' tail shortening by E. coli ribonuclease E. Nature. 1998 Jan 1;391(6662):99–102. [PubMed]
  • Iost I, Dreyfus M. The stability of Escherichia coli lacZ mRNA depends upon the simultaneity of its synthesis and translation. EMBO J. 1995 Jul 3;14(13):3252–3261. [PMC free article] [PubMed]
  • Jain C, Kleckner N. IS10 mRNA stability and steady state levels in Escherichia coli: indirect effects of translation and role of rne function. Mol Microbiol. 1993 Jul;9(2):233–247. [PubMed]
  • Keiler KC, Waller PR, Sauer RT. Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science. 1996 Feb 16;271(5251):990–993. [PubMed]
  • Kunkel TA, Roberts JD, Zakour RA. Rapid and efficient site-specific mutagenesis without phenotypic selection. Methods Enzymol. 1987;154:367–382. [PubMed]
  • Lerner CG, Inouye M. Low copy number plasmids for regulated low-level expression of cloned genes in Escherichia coli with blue/white insert screening capability. Nucleic Acids Res. 1990 Aug 11;18(15):4631–4631. [PMC free article] [PubMed]
  • Mackie GA. Posttranscriptional regulation of ribosomal protein S20 and stability of the S20 mRNA species. J Bacteriol. 1987 Jun;169(6):2697–2701. [PMC free article] [PubMed]
  • Mackie GA, Genereaux JL. The role of RNA structure in determining RNase E-dependent cleavage sites in the mRNA for ribosomal protein S20 in vitro. J Mol Biol. 1993 Dec 20;234(4):998–1012. [PubMed]
  • Mackie GA, Genereaux JL, Masterman SK. Modulation of the activity of RNase E in vitro by RNA sequences and secondary structures 5' to cleavage sites. J Biol Chem. 1997 Jan 3;272(1):609–616. [PubMed]
  • Makarova OV, Makarov EM, Sousa R, Dreyfus M. Transcribing of Escherichia coli genes with mutant T7 RNA polymerases: stability of lacZ mRNA inversely correlates with polymerase speed. Proc Natl Acad Sci U S A. 1995 Dec 19;92(26):12250–12254. [PMC free article] [PubMed]
  • McDowall KJ, Kaberdin VR, Wu SW, Cohen SN, Lin-Chao S. Site-specific RNase E cleavage of oligonucleotides and inhibition by stem-loops. Nature. 1995 Mar 16;374(6519):287–290. [PubMed]
  • Naureckiene S, Uhlin BE. In vitro analysis of mRNA processing by RNase E in the pap operon of Escherichia coli. Mol Microbiol. 1996 Jul;21(1):55–68. [PubMed]
  • Nilsson G, Belasco JG, Cohen SN, von Gabain A. Effect of premature termination of translation on mRNA stability depends on the site of ribosome release. Proc Natl Acad Sci U S A. 1987 Jul;84(14):4890–4894. [PMC free article] [PubMed]
  • Nilsson P, Naureckiene S, Uhlin BE. Mutations affecting mRNA processing and fimbrial biogenesis in the Escherichia coli pap operon. J Bacteriol. 1996 Feb;178(3):683–690. [PMC free article] [PubMed]
  • O'Hara EB, Chekanova JA, Ingle CA, Kushner ZR, Peters E, Kushner SR. Polyadenylylation helps regulate mRNA decay in Escherichia coli. Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):1807–1811. [PMC free article] [PubMed]
  • Philippe C, Eyermann F, Bénard L, Portier C, Ehresmann B, Ehresmann C. Ribosomal protein S15 from Escherichia coli modulates its own translation by trapping the ribosome on the mRNA initiation loading site. Proc Natl Acad Sci U S A. 1993 May 15;90(10):4394–4398. [PMC free article] [PubMed]
  • Plumbridge JA, Dondon J, Nakamura Y, Grunberg-Manago M. Effect of NusA protein on expression of the nusA,infB operon in E. coli. Nucleic Acids Res. 1985 May 10;13(9):3371–3388. [PMC free article] [PubMed]
  • Portier C, Dondon L, Grunberg-Manago M. Translational autocontrol of the Escherichia coli ribosomal protein S15. J Mol Biol. 1990 Jan 20;211(2):407–414. [PubMed]
  • Py B, Higgins CF, Krisch HM, Carpousis AJ. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature. 1996 May 9;381(6578):169–172. [PubMed]
  • Rapaport LR, Mackie GA. Influence of translational efficiency on the stability of the mRNA for ribosomal protein S20 in Escherichia coli. J Bacteriol. 1994 Feb;176(4):992–998. [PMC free article] [PubMed]
  • Régnier P, Hajnsdorf E. Decay of mRNA encoding ribosomal protein S15 of Escherichia coli is initiated by an RNase E-dependent endonucleolytic cleavage that removes the 3' stabilizing stem and loop structure. J Mol Biol. 1991 Jan 20;217(2):283–292. [PubMed]
  • Régnier P, Portier C. Initiation, attenuation and RNase III processing of transcripts from the Escherichia coli operon encoding ribosomal protein S15 and polynucleotide phosphorylase. J Mol Biol. 1986 Jan 5;187(1):23–32. [PubMed]
  • Régnier P, Grunberg-Manago M, Portier C. Nucleotide sequence of the pnp gene of Escherichia coli encoding polynucleotide phosphorylase. Homology of the primary structure of the protein with the RNA-binding domain of ribosomal protein S1. J Biol Chem. 1987 Jan 5;262(1):63–68. [PubMed]
  • Simons RW, Houman F, Kleckner N. Improved single and multicopy lac-based cloning vectors for protein and operon fusions. Gene. 1987;53(1):85–96. [PubMed]
  • Singer P, Nomura M. Stability of ribosomal protein mRNA and translational feedback regulation in Escherichia coli. Mol Gen Genet. 1985;199(3):543–546. [PubMed]
  • Springer M, Plumbridge JA, Butler JS, Graffe M, Dondon J, Mayaux JF, Fayat G, Lestienne P, Blanquet S, Grunberg-Manago M. Autogenous control of Escherichia coli threonyl-tRNA synthetase expression in vivo. J Mol Biol. 1985 Sep 5;185(1):93–104. [PubMed]
  • Steitz JA. Polypeptide chain initiation: nucleotide sequences of the three ribosomal binding sites in bacteriophage R17 RNA. Nature. 1969 Dec 6;224(5223):957–964. [PubMed]
  • Xu F, Lin-Chao S, Cohen SN. The Escherichia coli pcnB gene promotes adenylylation of antisense RNAI of ColE1-type plasmids in vivo and degradation of RNAI decay intermediates. Proc Natl Acad Sci U S A. 1993 Jul 15;90(14):6756–6760. [PMC free article] [PubMed]
  • Yano R, Yura T. Suppression of the Escherichia coli rpoH opal mutation by ribosomes lacking S15 protein. J Bacteriol. 1989 Mar;171(3):1712–1717. [PMC free article] [PubMed]
  • Yarchuk O, Iost I, Dreyfus M. The relation between translation and mRNA degradation in the lacZ gene. Biochimie. 1991 Dec;73(12):1533–1541. [PubMed]
  • Zilhão R, Camelo L, Arraiano CM. DNA sequencing and expression of the gene rnb encoding Escherichia coli ribonuclease II. Mol Microbiol. 1993 Apr;8(1):43–51. [PubMed]
  • Zilhão R, Plumbridge J, Hajnsdorf E, Régnier P, Arraiano CM. Escherichia coli RNase II: characterization of the promoters involved in the transcription of rnb. Microbiology. 1996 Feb;142(Pt 2):367–375. [PubMed]

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