• Müller, C., Crowe-McAuliffe, C. & Wilson, D. N. Ribosome rescue pathways in bacteria. Front. Microbiol. 12, 652980 (2021).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Ivanova, N., Pavlov, M. Y., Felden, B. & Ehrenberg, M. Ribosome rescue by tmRNA requires truncated mRNAs. J. Mol. Biol. 338, 33–41 (2004).

    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    CAS 
    PubMed 

    Google Scholar
     

  • Subramaniam, A. R., Zid, B. M. & O’Shea, E. K. An integrated approach reveals regulatory controls on bacterial translation elongation. Cell 159, 1200–1211 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

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

    CAS 
    PubMed 

    Google Scholar
     

  • Yan, L. L. & Zaher, H. S. How do cells cope with RNA damage and its consequences? J. Biol. Chem. 294, 15158–15171 (2019).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Thomas, E. N., Kim, K. Q., McHugh, E. P., Marcinkiewicz, T. & Zaher, H. S. Alkylative damage of mRNA leads to ribosome stalling and rescue by trans translation in bacteria. eLife 9, e61984 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

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

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • 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).

    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    CAS 
    PubMed 

    Google Scholar
     

  • 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).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ikeuchi, K. et al. Collided ribosomes form a unique structural interface to induce Hel2-driven quality control pathways. EMBO J. 38, e100276 (2019).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Juszkiewicz, S. et al. ZNF598 is a quality control sensor of collided ribosomes. Mol. Cell 72, 469–481 (2018).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Matsuo, Y. et al. Ubiquitination of stalled ribosome triggers ribosome-associated quality control. Nat. Commun. 8, 159 (2017).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Simms, C. L., Yan, L. L. & Zaher, H. S. Ribosome collision is critical for quality control during no-go decay. Mol. Cell 68, 361–373 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Langridge, G. C. et al. Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res. 19, 2308–2316 (2009).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Kannan, K. et al. The general mode of translation inhibition by macrolide antibiotics. Proc. Natl Acad. Sci. USA 111, 15958–15963 (2014).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Beckert, B. et al. Structural and mechanistic basis for translation inhibition by macrolide and ketolide antibiotics. Nat. Commun. 12, 4466 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zhou, W. et al. PPR-SMR protein SOT1 has RNA endonuclease activity. Proc. Natl Acad. Sci. USA 114, E1554–E1563 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wu, W. J. et al. SOT1, a pentatricopeptide repeat protein with a small MutS-related domain, is required for correct processing of plastid 23S-4.5S rRNA precursors in Arabidopsis thaliana. Plant J. 85, 607–621 (2016).

    CAS 
    PubMed 

    Google Scholar
     

  • D’Orazio, K. N. et al. The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during no go decay. eLife 8, e49117 (2019).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Liu, S., Melonek, J., Boykin, L. M., Small, I. & Howell, K. A. PPR-SMRs: ancient proteins with enigmatic functions. RNA Biol. 10, 1501–1510 (2013).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Glover, M. L. et al. NONU-1 encodes a conserved endonuclease required for mRNA translation surveillance. Cell Rep. 30, 4321–4331 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mohammad, F., Green, R. & Buskirk, A. R. A systematically-revised ribosome profiling method for bacteria reveals pauses at single-codon resolution. eLife 8, e42591 (2019).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chiba, S., Lamsa, A. & Pogliano, K. A ribosome-nascent chain sensor of membrane protein biogenesis in Bacillus subtilis. EMBO J. 28, 3461–3475 (2009).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ishii, E. et al. Nascent chain-monitored remodeling of the Sec machinery for salinity adaptation of marine bacteria. Proc. Natl Acad. Sci. USA 112, E5513–E5522 (2015).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Su, T. et al. The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling. eLife 6, e25642 (2017).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schuwirth, B. S. et al. Structures of the bacterial ribosome at 3.5 Å resolution. Science 310, 827–834 (2005).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Selmer, M., Gao, Y. G., Weixlbaumer, A. & Ramakrishnan, V. Ribosome engineering to promote new crystal forms. Acta Crystallogr. D 68, 578–583 (2012).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Atkins, J. F. & Bjork, G. R. A gripping tale of ribosomal frameshifting: extragenic suppressors of frameshift mutations spotlight P-site realignment. Microbiol. Mol. Biol. R. 73, 178 (2009).

    CAS 

    Google Scholar
     

  • Beckert, B. et al. Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization. EMBO J. 36, 2061–2072 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Beckert, B. et al. Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1. Nat. Microbiol. 3, 1115 (2018).

    CAS 
    PubMed 

    Google Scholar
     

  • Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Ferrin, M. A. & Subramaniam, A. R. Kinetic modeling predicts a stimulatory role for ribosome collisions at elongation stall sites in bacteria. eLife 6, e23629 (2017).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Simms, C. L., Yan, L. L., Qiu, J. K. & Zaher, H. S. Ribosome collisions result in +1 frameshifting in the absence of no-go decay. Cell Rep. 28, 1679–1689 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Smith, A. M., Costello, M. S., Kettring, A. H., Wingo, R. J. & Moore, S. D. Ribosome collisions alter frameshifting at translational reprogramming motifs in bacterial mRNAs. Proc. Natl Acad. Sci. USA 116, 21769–21779 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chai, Q. et al. Organization of ribosomes and nucleoids in Escherichia coli cells during growth and in quiescence. J. Biol. Chem. 289, 11342–11352 (2014).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Crameri, A., Whitehorn, E. A., Tate, E. & Stemmer, W. P. C. Improved green fluorescent protein by molecular evolution using DNA shuffling. Nat. Biotechnol. 14, 315–319 (1996).

    CAS 
    PubMed 

    Google Scholar
     

  • Jiang, H. S., Lei, R., Ding, S. W. & Zhu, S. F. Skewer: a fast and accurate adapter trimmer for next-generation sequencing paired-end reads. BMC Bioinformatics 15, 182 (2014).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).


    Google Scholar
     

  • Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Eddy, S. R. A new generation of homology search tools based on probabilistic inference. Genome Inform. 23, 205–211 (2009).

    PubMed 

    Google Scholar
     

  • Finn, R. D. et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 44, D279–D285 (2016).

    CAS 
    PubMed 

    Google Scholar
     

  • Lassmann, T., Frings, O. & Sonnhammer, E. L. L. Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic Acids Res. 37, 858–865 (2009).

    CAS 
    PubMed 

    Google Scholar
     

  • Cole, C., Barber, J. D. & Barton, G. J. The Jpred 3 secondary structure prediction server. Nucleic Acids Res. 36, W197–W201 (2008).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Price, M. N., Dehal, P. S. & Arkin, A. P. FastTree 2—approximately maximum-likelihood trees for large alignments. PLoS ONE 5, e9490 (2010).

    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Shevchenko, A., Wilm, M., Vorm, O. & Mann, M. Mass spectrometric sequencing of proteins from silver stained polyacrylamide gels. Anal. Chem. 68, 850–858 (1996).

    CAS 
    PubMed 

    Google Scholar
     

  • Sohmen, D. et al. Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling. Nat. Commun. 6, 6941 (2015).

    ADS 
    CAS 
    PubMed 

    Google Scholar
     

  • Schafer, H. et al. The alarmones (p)ppGpp are part of the heat shock response of Bacillus subtilis. PLoS Genet. 16, e1008275 (2020).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wells, J. N. et al. Structure and function of yeast Lso2 and human CCDC124 bound to hibernating ribosomes. PLoS Biol. 18, e3000780 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).

    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zivanov, J., Nakane, T. & Scheres, S. H. W. Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1. IUCrJ 7, 253–267 (2020).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Loveland, A. B., Demo, G. & Korostelev, A. A. Cryo-EM of elongating ribosome with EFTu-GTP elucidates tRNA proofreading. Nature 584, 640–645 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Byrne, R. T., Konevega, A. L., Rodnina, M. V. & Antson, A. A. The crystal structure of unmodified tRNAPhe from Escherichia coli. Nucleic Acids Res. 38, 4154–4162 (2010).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Loveland, A. B. & Korostelev, A. A. Structural dynamics of protein S1 on the 70S ribosome visualized by ensemble cryo-EM. Methods 137, 55–66 (2018).

    CAS 
    PubMed 

    Google Scholar
     

  • Mirdita, M., Steinegger, M. & Soding, J. MMseqs2 desktop and local web server app for fast, interactive sequence searches. Bioinformatics 35, 2856–2858 (2019).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D 60, 2126–2132 (2004).

    PubMed 

    Google Scholar
     

  • Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).

    CAS 
    PubMed 

    Google Scholar
     



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