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. 1996 May 1;24(9):1753–1757. doi: 10.1093/nar/24.9.1753

Accumulation of a mRNA decay intermediate by ribosomal pausing at a stop codon.

A Björnsson 1, L A Isaksson 1
PMCID: PMC145836  PMID: 8649996

Abstract

A RNA fragment which is protected from degradation by ribosome pausing at a stop codon has been identified in growing Escherichia coli. The fragment is 261 nt long and corresponds to the 3'-end of the mRNA expressed from a semi-synthetic model gene. The 5'-end of the RNA fragment, denoted rpRNA (ribosomal pause RNA), is located 13 bases upstream of the stop codon. In vivo decay of the complete mRNA and accumulation of rpRNA are dependent on the nature of the stop codon and its codon context. The data indicate that the rpRNA fragment arises from interrupted decay of the S3A'mRNA in the 5'-->m3'direction, in connection with a ribosomal pause at the stop codon. RF-2 decoding of UGA is less efficient than RF-1 decoding of UAG in identical codon contexts, as judged from rpRNA steady-state levels. The half-life of UGA-containing rpRNAs is at least 5 min, indicating that ribosomal pausing can be a major factor in stabilising downstream regions of messenger RNAs.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Adhya S., Gottesman M. Control of transcription termination. Annu Rev Biochem. 1978;47:967–996. doi: 10.1146/annurev.bi.47.070178.004535. [DOI] [PubMed] [Google Scholar]
  2. Alexieva Z., Duvall E. J., Ambulos N. P., Jr, Kim U. J., Lovett P. S. Chloramphenicol induction of cat-86 requires ribosome stalling at a specific site in the leader. Proc Natl Acad Sci U S A. 1988 May;85(9):3057–3061. doi: 10.1073/pnas.85.9.3057. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Baracchini E., Bremer H. Determination of synthesis rate and lifetime of bacterial mRNAs. Anal Biochem. 1987 Dec;167(2):245–260. doi: 10.1016/0003-2697(87)90160-6. [DOI] [PubMed] [Google Scholar]
  4. Bechhofer D. H., Dubnau D. Induced mRNA stability in Bacillus subtilis. Proc Natl Acad Sci U S A. 1987 Jan;84(2):498–502. doi: 10.1073/pnas.84.2.498. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Björnsson A., Isaksson L. A. UGA codon context which spans three codons. Reversal by ms2i6A37 in tRNA, mutation in rpsD(S4) or streptomycin. J Mol Biol. 1993 Aug 20;232(4):1017–1029. doi: 10.1006/jmbi.1993.1457. [DOI] [PubMed] [Google Scholar]
  6. Cannistraro V. J., Kennell D. Evidence that the 5' end of lac mRNA starts to decay as soon as it is synthesized. J Bacteriol. 1985 Feb;161(2):820–822. doi: 10.1128/jb.161.2.820-822.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Carpousis A. J., Van Houwe G., Ehretsmann C., Krisch H. M. 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. doi: 10.1016/0092-8674(94)90363-8. [DOI] [PubMed] [Google Scholar]
  8. Coulondre C., Miller J. H. Genetic studies of the lac repressor. III. Additional correlation of mutational sites with specific amino acid residues. J Mol Biol. 1977 Dec 15;117(3):525–567. doi: 10.1016/0022-2836(77)90056-0. [DOI] [PubMed] [Google Scholar]
  9. Eggertsson G., Söll D. Transfer ribonucleic acid-mediated suppression of termination codons in Escherichia coli. Microbiol Rev. 1988 Sep;52(3):354–374. doi: 10.1128/mr.52.3.354-374.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Ehretsmann C. P., Carpousis A. J., Krisch H. M. mRNA degradation in procaryotes. FASEB J. 1992 Oct;6(13):3186–3192. doi: 10.1096/fasebj.6.13.1397840. [DOI] [PubMed] [Google Scholar]
  11. Faxén M., Plumbridge J., Isaksson L. A. Codon choice and potential complementarity between mRNA downstream of the initiation codon and bases 1471-1480 in 16S ribosomal RNA affects expression of glnS. Nucleic Acids Res. 1991 Oct 11;19(19):5247–5251. doi: 10.1093/nar/19.19.5247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Kirsebom L. A., Isaksson L. A. Involvement of ribosomal protein L7/L12 in control of translational accuracy. Proc Natl Acad Sci U S A. 1985 Feb;82(3):717–721. doi: 10.1073/pnas.82.3.717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. McCormick J. R., Zengel J. M., Lindahl L. Correlation of translation efficiency with the decay of lacZ mRNA in Escherichia coli. J Mol Biol. 1994 Jun 24;239(5):608–622. doi: 10.1006/jmbi.1994.1403. [DOI] [PubMed] [Google Scholar]
  14. Mikuni O., Kawakami K., Nakamura Y. Sequence and functional analysis of mutations in the gene encoding peptide-chain-release factor 2 of Escherichia coli. Biochimie. 1991 Dec;73(12):1509–1516. doi: 10.1016/0300-9084(91)90185-4. [DOI] [PubMed] [Google Scholar]
  15. Miller J. H., Albertini A. M. Effects of surrounding sequence on the suppression of nonsense codons. J Mol Biol. 1983 Feb 15;164(1):59–71. doi: 10.1016/0022-2836(83)90087-6. [DOI] [PubMed] [Google Scholar]
  16. Miller J. H., Coulondre C., Farabaugh P. J. Correlation of nonsense sites in the lacI gene with specific codons in the nucleotide sequence. Nature. 1978 Aug 24;274(5673):770–775. doi: 10.1038/274770a0. [DOI] [PubMed] [Google Scholar]
  17. Morse D. E., Yanofsky C. Polarity and the degradation of mRNA. Nature. 1969 Oct 25;224(5217):329–331. doi: 10.1038/224329a0. [DOI] [PubMed] [Google Scholar]
  18. Mottagui-Tabar S., Björnsson A., Isaksson L. A. The second to last amino acid in the nascent peptide as a codon context determinant. EMBO J. 1994 Jan 1;13(1):249–257. doi: 10.1002/j.1460-2075.1994.tb06255.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Neidhardt F. C., Bloch P. L., Smith D. F. Culture medium for enterobacteria. J Bacteriol. 1974 Sep;119(3):736–747. doi: 10.1128/jb.119.3.736-747.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Nilsson B., Moks T., Jansson B., Abrahmsén L., Elmblad A., Holmgren E., Henrichson C., Jones T. A., Uhlén M. A synthetic IgG-binding domain based on staphylococcal protein A. Protein Eng. 1987 Feb-Mar;1(2):107–113. doi: 10.1093/protein/1.2.107. [DOI] [PubMed] [Google Scholar]
  21. Nilsson G., Belasco J. G., Cohen S. N., 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. doi: 10.1073/pnas.84.14.4890. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. O'Hara E. B., Chekanova J. A., Ingle C. A., Kushner Z. R., Peters E., Kushner S. R. Polyadenylylation helps regulate mRNA decay in Escherichia coli. Proc Natl Acad Sci U S A. 1995 Mar 14;92(6):1807–1811. doi: 10.1073/pnas.92.6.1807. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Peltz S. W., Brown A. H., Jacobson A. mRNA destabilization triggered by premature translational termination depends on at least three cis-acting sequence elements and one trans-acting factor. Genes Dev. 1993 Sep;7(9):1737–1754. doi: 10.1101/gad.7.9.1737. [DOI] [PubMed] [Google Scholar]
  24. Py B., Causton H., Mudd E. A., Higgins C. F. A protein complex mediating mRNA degradation in Escherichia coli. Mol Microbiol. 1994 Nov;14(4):717–729. doi: 10.1111/j.1365-2958.1994.tb01309.x. [DOI] [PubMed] [Google Scholar]
  25. Rapaport L. R., Mackie G. A. 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. doi: 10.1128/jb.176.4.992-998.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Sørensen M. A., Pedersen S. Absolute in vivo translation rates of individual codons in Escherichia coli. The two glutamic acid codons GAA and GAG are translated with a threefold difference in rate. J Mol Biol. 1991 Nov 20;222(2):265–280. doi: 10.1016/0022-2836(91)90211-n. [DOI] [PubMed] [Google Scholar]
  27. Tate W. P., Brown C. M. Translational termination: "stop" for protein synthesis or "pause" for regulation of gene expression. Biochemistry. 1992 Mar 10;31(9):2443–2450. doi: 10.1021/bi00124a001. [DOI] [PubMed] [Google Scholar]
  28. Vind J., Sørensen M. A., Rasmussen M. D., Pedersen S. Synthesis of proteins in Escherichia coli is limited by the concentration of free ribosomes. Expression from reporter genes does not always reflect functional mRNA levels. J Mol Biol. 1993 Jun 5;231(3):678–688. doi: 10.1006/jmbi.1993.1319. [DOI] [PubMed] [Google Scholar]
  29. Wagner L. A., Gesteland R. F., Dayhuff T. J., Weiss R. B. An efficient Shine-Dalgarno sequence but not translation is necessary for lacZ mRNA stability in Escherichia coli. J Bacteriol. 1994 Mar;176(6):1683–1688. doi: 10.1128/jb.176.6.1683-1688.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Wolin S. L., Walter P. Ribosome pausing and stacking during translation of a eukaryotic mRNA. EMBO J. 1988 Nov;7(11):3559–3569. doi: 10.1002/j.1460-2075.1988.tb03233.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Xu F., Cohen S. N. RNA degradation in Escherichia coli regulated by 3' adenylation and 5' phosphorylation. Nature. 1995 Mar 9;374(6518):180–183. doi: 10.1038/374180a0. [DOI] [PubMed] [Google Scholar]
  32. Yarchuk O., Jacques N., Guillerez J., Dreyfus M. Interdependence of translation, transcription and mRNA degradation in the lacZ gene. J Mol Biol. 1992 Aug 5;226(3):581–596. doi: 10.1016/0022-2836(92)90617-s. [DOI] [PubMed] [Google Scholar]
  33. von Gabain A., Belasco J. G., Schottel J. L., Chang A. C., Cohen S. N. Decay of mRNA in Escherichia coli: investigation of the fate of specific segments of transcripts. Proc Natl Acad Sci U S A. 1983 Feb;80(3):653–657. doi: 10.1073/pnas.80.3.653. [DOI] [PMC free article] [PubMed] [Google Scholar]

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