Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Mechanisms of ribosome rescue in bacteria

Nature Reviews Microbiology volume 13, pages 285–297 (2015)Cite this article

Subjects

Key Points

  • Bacterial ribosomes that are stalled at the end of an mRNA that lack a stop codon cannot be released by the translation termination factors peptide chain release factor 1 (RF1) and RF2. Ribosomes in these non-stop translation complexes must be rescued to maintain the protein synthesis capacity of the cell.

  • The primary pathway used by bacteria to rescue ribosomes stalled in non-stop complexes is trans-translation, which results in release of the ribosome and degradation of the nascent polypeptide and the mRNA.

  • Some bacteria have the alternative ribosome-rescue factor A (ArfA) or ArfB pathways as a backup for trans-translation. ArfA recruits RF2 to rescue ribosomes, and ArfB functions directly to hydrolyse the peptidyl-tRNA and rescue the ribosome.

  • Ribosomes stalled in the middle of an mRNA can be targeted for rescue if the mRNA is cleaved to produce a non-stop complex, or they can resume elongation. Ribosomes stalled as part of a regulatory programme for gene expression are protected from rescue mechanisms.

  • The broadly conserved translation elongation factor EF-P promotes translation through polyproline sequences and reduces the number of ribosomes that must be rescued.

Abstract

Ribosomes that stall during translation need to be rescued to ensure that the protein synthesis capacity of the cell is maintained. Stalling arises when ribosomes become trapped at the 3′ end of an mRNA, which occurs when a codon is unavailable, as this leads to the arrest of elongation or termination. In addition, various factors can induce ribosome stalling in the middle of an mRNA, including the presence of specific amino acid sequence motifs in the nascent polypeptide. Almost all bacteria use a mechanism known as trans-translation to rescue stalled ribosomes, and some species also have other rescue mechanisms that are mediated either by the alternative ribosome-rescue factor A (ArfA) or ArfB. In this Review, I summarize the recent studies that have demonstrated the conditions that trigger ribosome stalling, the pathways that bacteria use to rescue stalled ribosomes and the physiological effects of these processes.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Triggers for translation stalling and ribosome rescue.
Figure 2: Ribosome rescue by trans-translation.
Figure 3: ArfA and ArfB: alternative pathways for ribosome rescue.
Figure 4: Elongation factor P promotes translation elongation.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Russell, J. B. & Cook, G. M. Energetics of bacterial growth: balance of anabolic and catabolic reactions. Microbiol. Rev. 59, 48–62 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Li, G.-W., Burkhardt, D., Gross, C. & Weissman, J. S. Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 157, 624–635 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Schmeing, T. M. & Ramakrishnan, V. What recent ribosome structures have revealed about the mechanism of translation. Nature 461, 1234–1242 (2009).

    Article  CAS  PubMed  Google Scholar 

  4. Siwiak, M. & Zielenkiewicz, P. Transimulation — protein biosynthesis web service. PLoS ONE 8, e73943 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Keiler, K. C. & Feaga, H. A. Resolving nonstop translation complexes is a matter of life or death. J. Bacteriol. 196, 2123–2130 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Ivanova, N., Pavlov, M. Y. & Ehrenberg, M. tmRNA-induced release of messenger RNA from stalled ribosomes. J. Mol. Biol. 350, 897–905 (2005).

    Article  CAS  PubMed  Google Scholar 

  7. Gonzalez de Valdivia, E. I. & Isaksson, L. A. Abortive translation caused by peptidyl-tRNA drop-off at NGG codons in the early coding region of mRNA. FEBS J. 272, 5306–5316 (2005).

    Article  CAS  PubMed  Google Scholar 

  8. Cruz-Vera, L. R., Magos-Castro, M. A., Zamora-Romo, E. & Guarneros, G. Ribosome stalling and peptidyl-tRNA drop-off during translational delay at AGA codons. Nucleic Acids Res. 32, 4462–4468 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Moore, S. D. & Sauer, R. T. Ribosome rescue: tmRNA tagging activity and capacity in Escherichia coli. Mol. Microbiol. 58, 456–466 (2005).

    Article  CAS  PubMed  Google Scholar 

  10. Ramadoss, N. S. et al. Small molecule inhibitors of trans-translation have broad-spectrum antibiotic activity. Proc. Natl Acad. Sci. USA 110, 10282–10287 (2013). This paper describes the identification of trans -translation inhibitors and demonstrates that they have antibacterial activity.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Ramadoss, N. S., Zhou, X. & Keiler, K. C. tmRNA is essential in Shigella flexneri. PLoS ONE 8, e57537 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Chadani, Y. et al. Ribosome rescue by Escherichia coli ArfA (YhdL) in the absence of trans-translation system. Mol. Microbiol. 78, 796–808 (2010). This paper describes the discovery of ArfA and demonstrates that at least one mechanism for ribosome rescue is required in E. coli.

    Article  PubMed  CAS  Google Scholar 

  13. Keiler, K. C., Waller, P. R. & Sauer, R. T. Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA. Science 271, 990–993 (1996). This paper describes the discovery of trans -translation.

    Article  CAS  PubMed  Google Scholar 

  14. Karzai, A. W., Susskind, M. M. & Sauer, R. T. SmpB, a unique RNA-binding protein essential for the peptide-tagging activity of SsrA (tmRNA). EMBO J. 18, 3793–3799 (1999). This study shows that SmpB binds to tmRNA and is required for trans -translation.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Bessho, Y. et al. Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA. Proc. Natl Acad. Sci. USA 104, 8293–8298 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Komine, Y., Kitabatake, M., Yokogawa, T., Nishikawa, K. & Inokuchi, H. A tRNA-like structure is present in 10Sa RNA, a small stable RNA from Escherichia coli. Proc. Natl Acad. Sci. USA 91, 9223–9227 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Yamamoto, Y., Sunohara, T., Jojima, K., Inada, T. & Aiba, H. SsrA-mediated trans-translation plays a role in mRNA quality control by facilitating degradation of truncated mRNAs. RNA 9, 408–418 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Hudson, C. M., Lau, B. Y. & Williams, K. P. Ends of the line for tmRNA–SmpB. Front. Microbiol. 5, 421 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  19. Shimizu, Y. ArfA recruits RF2 into stalled ribosomes. J. Mol. Biol. 423, 624–631 (2012).

    Article  CAS  PubMed  Google Scholar 

  20. Chadani, Y., Ono, K., Kutsukake, K. & Abo, T. Escherichia coli YaeJ protein mediates a novel ribosome-rescue pathway distinct from SsrA- and ArfA-mediated pathways. Mol. Microbiol. 80, 772–785 (2011). This paper describes the discovery of ArfB.

    Article  CAS  PubMed  Google Scholar 

  21. Kurita, D., Chadani, Y., Muto, A., Abo, T. & Himeno, H. ArfA recognizes the lack of mRNA in the mRNA channel after RF2 binding for ribosome rescue. Nucleic Acids Res. 42, 13339–13352 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Ivanova, N., Pavlov, M. Y., Felden, B. & Ehrenberg, M. Ribosome rescue by tmRNA requires truncated mRNAs. J. Mol. Biol. 338, 33–41 (2004). This paper presents in vitro assays that show that trans -translation is much faster when the mRNA does not extend past the leading edge of the ribosome.

    Article  CAS  PubMed  Google Scholar 

  23. Moore, S. D. & Sauer, R. T. The tmRNA system for translational surveillance and ribosome rescue. Annu. Rev. Biochem. 76, 101–124 (2007).

    Article  CAS  PubMed  Google Scholar 

  24. Li, G.-W., Oh, E. & Weissman, J. S. The anti-Shine–Dalgarno sequence drives translational pausing and codon choice in bacteria. Nature 484, 538–541 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Schrader, J. M. et al. The coding and noncoding architecture of the Caulobacter crescentus genome. PLoS Genet. 10, e1004463 (2014).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  26. Shoji, S., Janssen, B. D., Hayes, C. S. & Fredrick, K. Translation factor LepA contributes to tellurite resistance in Escherichia coli but plays no apparent role in the fidelity of protein synthesis. Biochimie 92, 157–163 (2010).

    Article  CAS  PubMed  Google Scholar 

  27. Elgamal, S. et al. EF-P dependent pauses integrate proximal and distal signals during translation. PLoS Genet. 10, e1004553 (2014). This study uses ribosome profiling to identify sites of translation stalling that can be relieved by EF-P.

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  28. Cruz-Vera, L. R., Sachs, M. S., Squires, C. L. & Yanofsky, C. Nascent polypeptide sequences that influence ribosome function. Curr. Opin. Microbiol. 14, 160–166 (2011).

    Article  CAS  PubMed  Google Scholar 

  29. Doerfel, L. K. et al. EF-P is essential for rapid synthesis of proteins containing consecutive proline residues. Science 339, 85–88 (2013).

    Article  CAS  PubMed  Google Scholar 

  30. Ude, S. et al. Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches. Science 339, 82–85 (2013). References 29 and 30 demonstrate that ribosomes stall at polyproline sequences in the absence of EF-P.

    Article  CAS  PubMed  Google Scholar 

  31. Li, X., Hirano, R., Tagami, H. & Aiba, H. Protein tagging at rare codons is caused by tmRNA action at the 3′ end of nonstop mRNA generated in response to ribosome stalling. RNA 12, 248–255 (2006).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  32. Li, X., Yokota, T., Ito, K., Nakamura, Y. & Aiba, H. Reduced action of polypeptide release factors induces mRNA cleavage and tmRNA tagging at stop codons in Escherichia coli. Mol. Microbiol. 63, 116–126 (2007).

    Article  CAS  PubMed  Google Scholar 

  33. Janssen, B. D., Garza-Sánchez, F. & Hayes, C. S. A-site mRNA cleavage is not required for tmRNA-mediated ssrA-peptide tagging. PLoS ONE 8, e81319 (2013).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Garza-Sánchez, F. et al. Amino acid starvation and colicin D treatment induce A-site mRNA cleavage in Escherichia coli. J. Mol. Biol. 378, 505–519 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  35. Hayes, C. S. & Sauer, R. T. Cleavage of the A site mRNA codon during ribosome pausing provides a mechanism for translational quality control. Mol. Cell 12, 903–911 (2003).

    Article  CAS  PubMed  Google Scholar 

  36. Sunohara, T., Jojima, K., Yamamoto, Y., Inada, T. & Aiba, H. Nascent-peptide-mediated ribosome stalling at a stop codon induces mRNA cleavage resulting in nonstop mRNA that is recognized by tmRNA. RNA 10, 378–386 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Sunohara, T., Jojima, K., Tagami, H., Inada, T. & Aiba, H. Ribosome stalling during translation elongation induces cleavage of mRNA being translated in Escherichia coli. J. Biol. Chem. 279, 15368–15375 (2004).

    Article  CAS  PubMed  Google Scholar 

  38. Garza-Sánchez, F., Shoji, S., Fredrick, K. & Hayes, C. S. RNase II is important for A-site mRNA cleavage during ribosome pausing. Mol. Microbiol. 73, 882–897 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  39. Pedersen, K. et al. The bacterial toxin RelE displays codon-specific cleavage of mRNAs in the ribosomal A site. Cell 112, 131–140 (2003).

    Article  CAS  PubMed  Google Scholar 

  40. Christensen, S. K., Pedersen, K., Hansen, F. G. & Gerdes, K. Toxin–antitoxin loci as stress-response-elements: ChpAK/MazF and ChpBK cleave translated RNAs and are counteracted by tmRNA. J. Mol. Biol. 332, 809–819 (2003).

    Article  CAS  PubMed  Google Scholar 

  41. Christensen, S. K. & Gerdes, K. RelE toxins from bacteria and Archaea cleave mRNAs on translating ribosomes, which are rescued by tmRNA. Mol. Microbiol. 48, 1389–1400 (2003). References 40 and 41show that toxin-mediated mRNA cleavage targets ribosomes to rescue pathways.

    Article  CAS  PubMed  Google Scholar 

  42. Doma, M. K. & Parker, R. RNA quality control in eukaryotes. Cell 131, 660–668 (2007).

    Article  CAS  PubMed  Google Scholar 

  43. Laursen, B. S., Sørensen, H. P., Mortensen, K. K. & Sperling-Petersen, H. U. Initiation of protein synthesis in bacteria. Microbiol. Mol. Biol. Rev. 69, 101–123 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  44. Ito, K. et al. Nascentome analysis uncovers futile protein synthesis in Escherichia coli. PLoS ONE 6, e28413 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Atkins, J. F. & Gesteland, R. F. A case for trans-translation. Nature 379, 769–771 (1996).

    Article  CAS  PubMed  Google Scholar 

  46. Gutmann, S. et al. Crystal structure of the transfer-RNA domain of transfer-messenger RNA in complex with SmpB. Nature 424, 699–703 (2003).

    Article  CAS  PubMed  Google Scholar 

  47. Ushida, C. et al. tRNA-like structures in 10Sa RNAs of Mycoplasma capricolum and Bacillus subtilis. Nucleic Acids Res. 22, 3392–3396 (1994).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Barends, S., Wower, J. & Kraal, B. Kinetic parameters for tmRNA binding to alanyl-tRNA synthetase and elongation factor Tu from Escherichia coli. Biochemistry 39, 2652–2658 (2000).

    Article  CAS  PubMed  Google Scholar 

  49. Rudinger-Thirion, J., Giegé, R. & Felden, B. Aminoacylated tmRNA from Escherichia coli interacts with prokaryotic elongation factor Tu. RNA 5, 989–992 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Felden, B., Himeno, H., Muto, A., Atkins, J. F. & Gesteland, R. F. Structural organization of Escherichia coli tmRNA. Biochimie 78, 979–983 (1996).

    Article  CAS  PubMed  Google Scholar 

  51. Tu, G. F., Reid, G. E., Zhang, J. G., Moritz, R. L. & Simpson, R. J. C-terminal extension of truncated recombinant proteins in Escherichia coli with a 10Sa RNA decapeptide. J. Biol. Chem. 270, 9322–9326 (1995).

    Article  CAS  PubMed  Google Scholar 

  52. Williams, K. P. & Bartel, D. P. Phylogenetic analysis of tmRNA secondary structure. RNA 2, 1306–1310 (1996).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Williams, K. P., Martindale, K. A. & Bartel, D. P. Resuming translation on tmRNA: a unique mode of determining a reading frame. EMBO J. 18, 5423–5433 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Keiler, K. C., Shapiro, L. & Williams, K. P. tmRNAs that encode proteolysis-inducing tags are found in all known bacterial genomes: a two-piece tmRNA functions in Caulobacter. Proc. Natl Acad. Sci. USA 97, 7778–7783 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Keiler, K. C. & Shapiro, L. tmRNA is required for correct timing of DNA replication in Caulobacter crescentus. J. Bacteriol. 185, 573–580 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Wiegert, T. & Schumann, W. SsrA-mediated tagging in Bacillus subtilis. J. Bacteriol. 183, 3885–3889 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Valle, M. et al. Visualizing tmRNA entry into a stalled ribosome. Science 300, 127–130 (2003).

    Article  CAS  PubMed  Google Scholar 

  58. Neubauer, C., Gillet, R., Kelley, A. C. & Ramakrishnan, V. Decoding in the absence of a codon by tmRNA and SmpB in the ribosome. Science 335, 1366–1369 (2012). This study shows how the tmRNA–SmpB complex recognizes the absence of an mRNA sequence beyond the decoding centre in a non-stop ribosome.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Kurita, D., Muto, A. & Himeno, H. Role of the C-terminal tail of SmpB in the early stage of trans-translation. RNA 16, 980–990 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Sundermeier, T. R., Dulebohn, D. P., Cho, H. J. & Karzai, A. W. A previously uncharacterized role for small protein B (SmpB) in transfer messenger RNA-mediated trans-translation. Proc. Natl Acad. Sci. USA 102, 2316–2321 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Miller, M. R. & Buskirk, A. R. An unusual mechanism for EF-Tu activation during tmRNA-mediated ribosome rescue. RNA 20, 228–235 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Kurita, D., Miller, M. R., Muto, A., Buskirk, A. R. & Himeno, H. Rejection of tmRNA·SmpB after GTP hydrolysis by EF-Tu on ribosomes stalled on intact mRNA. RNA 20, 1706–1714 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  63. Weis, F. et al. tmRNA–SmpB: a journey to the centre of the bacterial ribosome. EMBO J. 29, 3810–3818 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Ramrath, D. J. et al. The complex of tmRNA–SmpB and EF-G on translocating ribosomes. Nature 485, 526–529 (2012).

    Article  CAS  PubMed  Google Scholar 

  65. Fu, J. et al. Visualizing the transfer-messenger RNA as the ribosome resumes translation. EMBO J. 29, 3819–3825 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Konno, T., Kurita, D., Takada, K., Muto, A. & Himeno, H. A functional interaction of SmpB with tmRNA for determination of the resuming point of trans-translation. RNA 13, 1723–1731 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Lee, S., Ishii, M., Tadaki, T., Muto, A. & Himeno, H. Determinants on tmRNA for initiating efficient and precise trans-translation: some mutations upstream of the tag-encoding sequence of Escherichia coli tmRNA shift the initiation point of trans-translation in vitro. RNA 7, 999–1012 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  68. Choy, J. S., Aung, L. L. & Karzai, A. W. Lon protease degrades transfer-messenger RNA-tagged proteins. J. Bacteriol. 189, 6564–6571 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Gottesman, S., Roche, E., Zhou, Y. & Sauer, R. T. The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system. Genes Dev. 12, 1338–1347 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Herman, C., Thévenet, D., Bouloc, P., Walker, G. C. & D'Ari, R. Degradation of carboxy-terminal-tagged cytoplasmic proteins by the Escherichia coli protease HflB (FtsH). Genes Dev. 12, 1348–1355 (1998).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  71. Flynn, J. M. et al. Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis. Proc. Natl Acad. Sci. USA 98, 10584–10589 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Richards, J., Mehta, P. & Karzai, A. W. RNase R degrades non-stop mRNAs selectively in an SmpB–tmRNA-dependent manner. Mol. Microbiol. 62, 1700–1712 (2006).

    Article  CAS  PubMed  Google Scholar 

  73. Mehta, P., Richards, J. & Karzai, A. W. tmRNA determinants required for facilitating nonstop mRNA decay. RNA 12, 2187–2198 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Venkataraman, K., Zafar, H. & Karzai, A. W. Distinct tmRNA sequence elements facilitate RNase R engagement on rescued ribosomes for selective nonstop mRNA decay. Nucleic Acids Res. 42, 11192–11202 (2015). This work demonstrates that sequences in tmRNA are required for RNase R-mediated degradation of non-stop mRNAs.

    Article  CAS  Google Scholar 

  75. Ge, Z., Mehta, P., Richards, J. & Karzai, A. W. Non-stop mRNA decay initiates at the ribosome. Mol. Microbiol. 78, 1159–1170 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Venkataraman, K., Guja, K. E., Garcia-Diaz, M. & Karzai, A. W. Non-stop mRNA decay: a special attribute of trans-translation mediated ribosome rescue. Front. Microbiol. 5, 93 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  77. Chadani, Y., Ito, K., Kutsukake, K. & Abo, T. ArfA recruits release factor 2 to rescue stalled ribosomes by peptidyl-tRNA hydrolysis in Escherichia coli. Mol. Microbiol. 86, 37–50 (2012).

    Article  CAS  PubMed  Google Scholar 

  78. Garza-Sánchez, F., Schaub, R. E., Janssen, B. D. & Hayes, C. S. tmRNA regulates synthesis of the ArfA ribosome rescue factor. Mol. Microbiol. 80, 1204–1219 (2011).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  79. Chadani, Y. et al. Trans-translation-mediated tight regulation of the expression of the alternative ribosome-rescue factor ArfA in Escherichia coli. Genes Genet. Syst. 86, 151–163 (2011).

    Article  CAS  PubMed  Google Scholar 

  80. Schaub, R. E., Poole, S. J., Garza-Sánchez, F., Benbow, S. & Hayes, C. S. Proteobacterial ArfA peptides are synthesized from non-stop messenger RNAs. J. Biol. Chem. 287, 29765–29775 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  81. Feaga, H. A., Viollier, P. H. & Keiler, K. C. Release of nonstop ribosomes is essential. mBio 5, e01916 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  82. Handa, Y., Inaho, N. & Nameki, N. YaeJ is a novel ribosome-associated protein in Escherichia coli that can hydrolyze peptidyl-tRNA on stalled ribosomes. Nucleic Acids Res. 39, 1739–1748 (2011).

    Article  CAS  PubMed  Google Scholar 

  83. Gagnon, M. G. et al. Structural basis for the rescue of stalled ribosomes: structure of YaeJ bound to the ribosome. Science 335, 1370–1372 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Kogure, H. et al. Identification of residues required for stalled-ribosome rescue in the codon-independent release factor YaeJ. Nucleic Acids Res. 42, 3152–3163 (2014).

    Article  CAS  PubMed  Google Scholar 

  85. Huang, C., Wolfgang, M. C., Withey, J., Koomey, M. & Friedman, D. I. Charged tmRNA but not tmRNA-mediated proteolysis is essential for Neisseria gonorrhoeae viability. EMBO J. 19, 1098–1107 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Personne, Y. & Parish, T. Mycobacterium tuberculosis possesses an unusual tmRNA rescue system. Tuberculosis (Edinb.) 94, 34–42 (2014).

    Article  CAS  Google Scholar 

  87. Thibonnier, M., Thiberge, J.-M. & De Reuse, H. Trans-translation in Helicobacter pylori: essentiality of ribosome rescue and requirement of protein tagging for stress resistance and competence. PLoS ONE 3, e3810 (2008).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  88. Fey, P. D. et al. A genetic resource for rapid and comprehensive phenotype screening of nonessential Staphylococcus aureus genes. mBio 4, e00537–12 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Chaudhuri, R. R. et al. Comprehensive identification of essential Staphylococcus aureus genes using transposon-mediated differential hybridisation (TMDH). BMC Genomics 10, 291 (2009).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  90. Glass, J. I. et al. Essential genes of a minimal bacterium. Proc. Natl Acad. Sci. USA 103, 425–430 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Keiler, K. C. Biology of trans-translation. Annu. Rev. Microbiol. 62, 133–151 (2008).

    Article  CAS  PubMed  Google Scholar 

  92. Abo, T., Ueda, K., Sunohara, T., Ogawa, K. & Aiba, H. SsrA-mediated protein tagging in the presence of miscoding drugs and its physiological role in Escherichia coli. Genes Cells 7, 629–638 (2002).

    Article  CAS  PubMed  Google Scholar 

  93. Li, J., Ji, L., Shi, W., Xie, J. & Zhang, Y. Trans-translation mediates tolerance to multiple antibiotics and stresses in Escherichia coli. J. Antimicrob. Chemother. 68, 2477–2481 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  94. Muto, A. et al. Requirement of transfer-messenger RNA for the growth of Bacillus subtilis under stresses. Genes Cells 5, 627–635 (2000).

    Article  CAS  PubMed  Google Scholar 

  95. Shin, J.-H. & Price, C. W. The SsrA–SmpB ribosome rescue system is important for growth of Bacillus subtilis at low and high temperatures. J. Bacteriol. 189, 3729–3737 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Julio, S. M., Heithoff, D. M. & Mahan, M. J. ssrA (tmRNA) plays a role in Salmonella enterica serovar Typhimurium pathogenesis. J. Bacteriol. 182, 1558–1563 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Svetlanov, A., Puri, N., Mena, P., Koller, A. & Karzai, A. W. Francisella tularensis tmRNA system mutants are vulnerable to stress, avirulent in mice, and provide effective immune protection. Mol. Microbiol. 85, 122–141 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Okan, N. A., Mena, P., Benach, J. L., Bliska, J. B. & Karzai, A. W. The smpB–ssrA mutant of Yersinia pestis functions as a live attenuated vaccine to protect mice against pulmonary plague infection. Infect. Immun. 78, 1284–1293 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Nudler, E., Avetissova, E., Markovtsov, V. & Goldfarb, A. Transcription processivity: protein–DNA interactions holding together the elongation complex. Science 273, 211–217 (1996).

    Article  CAS  PubMed  Google Scholar 

  100. Bandyra, K. J. & Luisi, B. F. Licensing and due process in the turnover of bacterial RNA. RNA Biol. 10, 627–635 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Zhang, Y. et al. MazF cleaves cellular mRNAs specifically at ACA to block protein synthesis in Escherichia coli. Mol. Cell 12, 913–923 (2003).

    Article  CAS  PubMed  Google Scholar 

  102. Maisonneuve, E., Shakespeare, L. J., Jørgensen, M. G. & Gerdes, K. Bacterial persistence by RNA endonucleases. Proc. Natl Acad. Sci. USA 108, 13206–13211 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Ueda, K. et al. Bacterial SsrA system plays a role in coping with unwanted translational readthrough caused by suppressor tRNAs. Genes Cells 7, 509–519 (2002).

    Article  CAS  PubMed  Google Scholar 

  104. Hayes, C. S., Bose, B. & Sauer, R. T. Proline residues at the C terminus of nascent chains induce SsrA tagging during translation termination. J. Biol. Chem. 277, 33825–33832 (2002).

    Article  CAS  PubMed  Google Scholar 

  105. Hayes, C. S., Bose, B. & Sauer, R. T. Stop codons preceded by rare arginine codons are efficient determinants of SsrA tagging in Escherichia coli. Proc. Natl Acad. Sci. USA 99, 3440–3445 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Caliskan, N., Katunin, V. I., Belardinelli, R., Peske, F. & Rodnina, M. V. Programmed-1 frameshifting by kinetic partitioning during impeded translocation. Cell 157, 1619–1631 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  107. Woolstenhulme, C. J. et al. Nascent peptides that block protein synthesis in bacteria. Proc. Natl Acad. Sci. USA 110, E878–E887 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Roche, E. D. & Sauer, R. T. SsrA-mediated peptide tagging caused by rare codons and tRNA scarcity. EMBO J. 18, 4579–4589 (1999).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Nakatogawa, H. & Ito, K. The ribosomal exit tunnel functions as a discriminating gate. Cell 108, 629–636 (2002).

    Article  CAS  PubMed  Google Scholar 

  110. Murakami, A., Nakatogawa, H. & Ito, K. Translation arrest of SecM is essential for the basal and regulated expression of SecA. Proc. Natl Acad. Sci. USA 101, 12330–12335 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. McNicholas, P., Salavati, R. & Oliver, D. Dual regulation of Escherichia coli secA translation by distinct upstream elements. J. Mol. Biol. 265, 128–141 (1997).

    Article  CAS  PubMed  Google Scholar 

  112. Garza-Sánchez, F., Janssen, B. D. & Hayes, C. S. Prolyl-tRNA(Pro) in the A-site of SecM-arrested ribosomes inhibits the recruitment of transfer-messenger RNA. J. Biol. Chem. 281, 34258–34268 (2006). This study shows that programmed stalls in translation can avoid ribosome rescue mechanisms.

    Article  PubMed  CAS  Google Scholar 

  113. Cruz-Vera, L. R., Rajagopal, S., Squires, C. & Yanofsky, C. Features of ribosome–peptidyl-tRNA interactions essential for tryptophan induction of tna operon expression. Mol. Cell 19, 333–343 (2005).

    Article  CAS  PubMed  Google Scholar 

  114. Hayes, C. S. & Keiler, K. C. Beyond ribosome rescue: tmRNA and co-translational processes. FEBS Lett. 584, 413–419 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Katz, A., Solden, L., Zou, S. B., Navarre, W. W. & Ibba, M. Molecular evolution of protein-RNA mimicry as a mechanism for translational control. Nucleic Acids Res. 42, 3261–3271 (2014).

    Article  CAS  PubMed  Google Scholar 

  116. Roy, H. et al. The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-β-lysine. Nature Chem. Biol. 7, 667–669 (2011).

    Article  CAS  Google Scholar 

  117. Blaha, G., Stanley, R. E. & Steitz, T. A. Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome. Science 325, 966–970 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  118. Peil, L. et al. Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P. Proc. Natl Acad. Sci. USA 110, 15265–15270 (2013). In this study, mass spectrometry was used to identify changes in the proteome caused by EF-P, and the stalling propensities of sequences flanking PP motifs were determined.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Starosta, A. L. et al. Translational stalling at polyproline stretches is modulated by the sequence context upstream of the stall site. Nucleic Acids Res. 42, 10711–10719 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Hersch, S. J. et al. Divergent protein motifs direct elongation factor P-mediated translational regulation in Salmonella enterica and Escherichia coli. mBio 4, e00180–13 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  121. Zou, S. B., Roy, H., Ibba, M. & Navarre, W. W. Elongation factor P mediates a novel post-transcriptional regulatory pathway critical for bacterial virulence. Virulence 2, 147–151 (2011).

    Article  PubMed  PubMed Central  Google Scholar 

  122. Zou, S. B. et al. Loss of elongation factor P disrupts bacterial outer membrane integrity. J. Bacteriol. 194, 413–425 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Hersch, S. J., Elgamal, S., Katz, A., Ibba, M. & Navarre, W. W. Translation initiation rate determines the impact of ribosome stalling on bacterial protein synthesis. J. Biol. Chem. 289, 28160–28171 (2014). This paper answers the question of why the abundance of some proteins that contain stalling sequences is not affected by the absence of EF-P.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Qin, Y. et al. The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome. Cell 127, 721–733 (2006).

    Article  CAS  PubMed  Google Scholar 

  125. Balakrishnan, R., Oman, K., Shoji, S., Bundschuh, R. & Fredrick, K. The conserved GTPase LepA contributes mainly to translation initiation in Escherichia coli. Nucleic Acids Res. 42, 13370–13383 (2014). This study uses ribosome profiling to show that EF4 does not affect translation stalling.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Russell, J. H. & Keiler, K. C. Subcellular localization of a bacterial regulatory RNA. Proc. Natl Acad. Sci. USA 106, 16405–16409 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Keiler, K. C. & Shapiro, L. tmRNA in Caulobacter crescentus is cell cycle regulated by temporally controlled transcription and RNA degradation. J. Bacteriol. 185, 1825–1830 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. Baranov, P. V. et al. Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons. Biol. Direct 1, 28 (2006).

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  129. Yamamoto, H. et al. EF-G and EF4: translocation and back-translocation on the bacterial ribosome. Nature Rev. Microbiol. 12, 89–100 (2014).

    Article  CAS  Google Scholar 

  130. Gagnon, M. G., Lin, J., Bulkley, D. & Steitz, T. A. Crystal structure of elongation factor 4 bound to a clockwise ratcheted ribosome. Science 345, 684–687 (2014).

    Article  CAS  PubMed  Google Scholar 

  131. Liu, H. et al. The conserved protein EF4 (LepA) modulates the elongation cycle of protein synthesis. Proc. Natl Acad. Sci. USA 108, 16223–16228 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Selmer, M. et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313, 1935–1942 (2006).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

K.C.K. was supported by grant GM68720 from the National Institutes of Health.

Author information

Authors and Affiliations

  1. Department of Biochemistry and Molecular Biology, 401 Althouse Laboratory, Pennsylvania State University, University Park, 16802, Pennsylvania, USA

    Kenneth C. Keiler

Authors
  1. Kenneth C. Keiler
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kenneth C. Keiler.

Ethics declarations

Competing interests

The author declares no competing financial interests.

Related links

PowerPoint slides

Glossary

Cognate aminoacyl-tRNA

A charged tRNA containing an anticodon that corresponds to a particular codon.

Splicing

The process of removing introns from a pre-mRNA transcript followed by the joining of exons to form a mature mRNA.

Polyadenylation

The addition of multiple adenosine residues to the 3′ end of an mRNA.

Frameshifting

A change in the reading frame of the ribosome during translation that alters the order in which the triplet nucleotides of the mRNA are recognized as codons.

Ribosome profiling

This technique (also known as ribo-seq) identifies ribosome footprints on mRNA using deep sequencing. Increased occupancy at one site on the mRNA compared with the footprints at other sites on the same mRNA is indicative of ribosome stalling.

Pseudoknots

RNA secondary structures that are formed by two stem-loop structures, in which the loop of one stem-loop forms half of the stem in the other stem-loop.

Transpeptidation

In the context of translation, the transfer of the nascent polypeptide from the tRNA in the P-site to the aminoacyl-tRNA in the A-site, which results in extension of the polypeptide by one amino acid.

A-site finger

The structure formed by helix 38 of 23S rRNA, which interacts with the A-site tRNA and forms a bridge between the large and small subunits of the ribosome.

Persister cells

Dormant or slow-growing populations of bacterial cells that are refractory to antibiotics.

Anti-Shine–Dalgarno element

The conserved sequence at the 3′ end of 16S rRNA that is complementary to the Shine–Dalgarno element found in the 5′ untranslated region of many mRNAs in Escherichia coli. This element is used for the positioning of the mRNA on the 30S subunit, and it has also been implicated in translation pausing.

Peptide exit tunnel

The tunnel in the 50S ribosomal subunit that is used for transfer of the nascent polypeptide from the peptidyl-transferase centre to the exterior of the ribosome.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Keiler, K. Mechanisms of ribosome rescue in bacteria. Nat Rev Microbiol 13, 285–297 (2015). https://doi.org/10.1038/nrmicro3438

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrmicro3438

Search

Advanced search

Quick links

Nature Briefing Microbiology

Sign up for the Nature Briefing: Microbiology newsletter — what matters in microbiology research, free to your inbox weekly.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing: Microbiology