Joazeiro, C. A. P. Ribosomal stalling during translation: providing substrates for ribosome-associated protein quality control. Annu. Rev. Cell Dev. Biol. 33, 343–368 (2017).
Google Scholar
Meydan, S. & Guydosh, N. R. A cellular handbook for collided ribosomes: surveillance pathways and collision types. Curr. Genet. 67, 19–26 (2021).
Google Scholar
Modrich, P. Mechanisms in E. coli and human mismatch repair (Nobel Lecture). Angew. Chem. Int. Ed. Engl. 55, 8490–8501 (2016).
Google Scholar
Moore, S. D. & Sauer, R. T. The tmRNA system for translational surveillance and ribosome rescue. Annu. Rev. Biochem. 76, 101–124 (2007).
Google Scholar
Joazeiro, C. A. P. Mechanisms and functions of ribosome-associated protein quality control. Nat. Rev. Mol. Cell Biol. 20, 368–383 (2019).
Google Scholar
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).
Google Scholar
Howard, C. J. & Frost, A. Ribosome-associated quality control and CAT tailing. Crit. Rev. Biochem. Mol. Biol. 56, 603–620 (2021).
Google Scholar
Lytvynenko, I. et al. Alanine tails signal proteolysis in bacterial ribosome-associated quality control. Cell 178, 76–90 (2019).
Google Scholar
D’Orazio, K. N. & Green, R. Ribosome states signal RNA quality control. Mol. Cell 81, 1372–1383 (2021).
Google Scholar
Vind, A. C., Genzor, A. V. & Bekker-Jensen, S. Ribosomal stress-surveillance: three pathways is a magic number. Nucleic Acids Res. 48, 10648–10661 (2020).
Google Scholar
Ikeuchi, K. et al. Collided ribosomes form a unique structural interface to induce Hel2‐driven quality control pathways. EMBO J. 38, 1–40 (2019).
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).
Google Scholar
Juszkiewicz, S. et al. ZNF598 is a quality control sensor of collided ribosomes. Mol. Cell 72, 469–481 (2018).
Google Scholar
Garzia, A. et al. The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs. Nat. Commun. 8, 16056 (2017).
Google Scholar
Sundaramoorthy, E. et al. ZNF598 and RACK1 regulate mammalian ribosome-associated quality control function by mediating regulatory 40S ribosomal ubiquitylation. Mol. Cell 65, 751–760 (2017).
Google Scholar
Juszkiewicz, S., Speldewinde, S. H., Wan, L., Svejstrup, J. Q. & Hegde, R. S. The ASC-1 complex disassembles collided ribosomes. Mol. Cell 79, 603–614 (2020).
Google Scholar
Matsuo, Y. et al. RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1. Nat. Struct. Mol. Biol. 27, 323–332 (2020).
Google Scholar
Matsuo, Y. et al. Ubiquitination of stalled ribosome triggers ribosome-associated quality control. Nat. Commun. 8, 159 (2017).
Google Scholar
Glover, M. L. et al. NONU-1 encodes a conserved endonuclease required for mRNA translation surveillance. Cell Rep. 30, 4321–4331 (2020).
Google Scholar
D’Orazio, K. N. et al. The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during no go decay. eLife 8, e49117 (2019).
Google Scholar
Nürenberg-Goloub, E. & Tampé, R. Ribosome recycling in mRNA translation, quality control, and homeostasis. Biol. Chem. 401, 47–61 (2019).
Google Scholar
Donaldson, K. M., Yin, H., Gekakis, N., Supek, F. & Joazeiro, C. A. P. Ubiquitin signals protein trafficking via interaction with a novel ubiquitin binding domain in the membrane fusion regulator, Vps9p. Curr. Biol. 13, 258–262 (2003).
Google Scholar
Burby, P. E. & Simmons, L. A. MutS2 promotes homologous recombination in Bacillus subtilis. J. Bacteriol. 199, e00682-16 (2017).
Google Scholar
Pinto, A. V. et al. Suppression of homologous and homeologous recombination by the bacterial MutS2 protein. Mol. Cell 17, 113–120 (2005).
Google Scholar
Hingorani, M. M. Mismatch binding, ADP–ATP exchange and intramolecular signaling during mismatch repair. DNA Repair 38, 24–31 (2016).
Google Scholar
Groothuizen, F. S. & Sixma, T. K. The conserved molecular machinery in DNA mismatch repair enzyme structures. DNA Repair 38, 14–23 (2016).
Google Scholar
Kyrpides, N. C., Woese, C. R. & Ouzounis, C. A. KOW: a novel motif linking a bacterial transcription factor with ribosomal proteins. Trends Biochem. Sci. 21, 425–426 (1996).
Google Scholar
Fukui, K. & Kuramitsu, S. Structure and function of the small MutS-related domain. Mol. Biol. Int. 2011, 691735 (2011).
Google Scholar
Sachadyn, P. Conservation and diversity of MutS proteins. Mutat. Res. 694, 20–30 (2010).
Google Scholar
Pochopien, A. A. et al. Structure of Gcn1 bound to stalled and colliding 80S ribosomes. Proc. Natl Acad. Sci. USA 118, e2022756118 (2021).
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).
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).
Google Scholar
Borovinskaya, M. A., Shoji, S., Holton, J. M., Fredrick, K. & Cate, J. H. D. A steric block in translation caused by the antibiotic spectinomycin. ACS Chem. Biol. 2, 545–552 (2007).
Google Scholar
Brodersen, D. E. et al. The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit. Cell 103, 1143–1154 (2000).
Google Scholar
Svetlov, M. S. et al. High-resolution crystal structures of ribosome-bound chloramphenicol and erythromycin provide the ultimate basis for their competition. RNA 25, 600–606 (2019).
Google Scholar
Filbeck, S. et al. Mimicry of canonical translation elongation underlies alanine tail synthesis in RQC. Mol. Cell 81, 104–114 (2021).
Google Scholar
Crowe-McAuliffe, C. et al. Structural basis for bacterial ribosome-associated quality control by RqcH and RqcP. Mol. Cell 81, 115–126 (2021).
Google Scholar
Takada, H. et al. RqcH and RqcP catalyze processive poly-alanine synthesis in a reconstituted ribosome-associated quality control system. Nucleic Acids Res. 49, 8355–8369 (2021).
Google Scholar
Thrun, A. et al. Convergence of mammalian RQC and C-end rule proteolytic pathways via alanine tailing. Mol. Cell 81, 2112–2122 (2021).
Google Scholar
Korostelev, A., Trakhanov, S., Laurberg, M. & Noller, H. F. Crystal structure of a 70S ribosome–tRNA complex reveals functional interactions and rearrangements. Cell 126, 1065–1077 (2006).
Google Scholar
Tejada-Arranz, A., de Crécy-Lagard, V. & de Reuse, H. Bacterial RNA degradosomes: molecular machines under tight control. Trends Biochem. Sci. 45, 42–57 (2020).
Google Scholar
Arnaud, M., Chastanet, A. & Débarbouillé, M. New vector for efficient allelic replacement in naturally nontransformable, low-GC-content, gram-positive bacteria. Appl. Environ. Microbiol. 70, 6887–6891 (2004).
Google Scholar
Koo, B.-M. et al. Construction and analysis of two genome-scale deletion libraries for Bacillus subtilis. Cell Syst. 4, 291–305 (2017).
Google Scholar
Mende, D. R. et al. proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. Nucleic Acids Res. 48, D621–D625 (2020).
Google Scholar
Bucher, P., Karplus, K., Moeri, N. & Hofmann, K. A flexible motif search technique based on generalized profiles. Comput. Chem. 20, 3–23 (1996).
Google Scholar
Levy, J. A., LaFlamme, C. W., Tsaprailis, G., Crynen, G. & Page, D. T. Dyrk1a mutations cause undergrowth of cortical pyramidal neurons via dysregulated growth factor signaling. Biol. Psychiatry 90, 295–306 (2021).
Google Scholar
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
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).
Google Scholar
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
Google Scholar
Crowe-McAuliffe, C. et al. Structural basis for antibiotic resistance mediated by the Bacillus subtilis ABCF ATPase VmlR. Proc. Natl Acad. Sci. USA 115, 8978–8983 (2018).
Google Scholar
Matzov, D. et al. The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus. Nat. Commun. 8, 723 (2017).
Google Scholar
Hoffman, D. W. et al. Crystal structure of prokaryotic ribosomal protein L9: a bi-lobed RNA-binding protein. EMBO J. 13, 205–212 (1994).
Google Scholar
Zimmermann, L. et al. A completely reimplemented MPI Bioinformatics Toolkit with a new HHpred server at its core. J. Mol. Biol. 430, 2237–2243 (2018).
Google Scholar
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).
Google Scholar
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).
Google Scholar
Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D 74, 519–530 (2018).
Google Scholar
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Google Scholar
Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N. & Sternberg, M. J. E. The Phyre2 web portal for protein modeling, prediction and analysis. Nat. Protoc. 10, 845–858 (2015).
Google Scholar
Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).
Google Scholar
Ribeiro, J. V. et al. QwikMD—integrative molecular dynamics toolkit for novices and experts. Sci. Rep. 6, 26536 (2016).
Google Scholar
Trabuco, L. G., Villa, E., Mitra, K., Frank, J. & Schulten, K. Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics. Structure 16, 673–683 (2008).
Google Scholar
Phillips, J. C. et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Chem. Phys. 153, 044130 (2020).
Google Scholar
Rundlet, E. J. et al. Structural basis of early translocation events on the ribosome. Nature 595, 741–745 (2021).
Google Scholar
Loveland, A. B., Demo, G. & Korostelev, A. A. Cryo-EM of elongating ribosome with EF-Tu•GTP elucidates tRNA proofreading. Nature 584, 640–645 (2020).
Google Scholar
Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).
Google Scholar
Amiri, H. & Noller, H. F. Structural evidence for product stabilization by the ribosomal mRNA helicase. RNA 25, 364–375 (2019).
Google Scholar
