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).
Meydan, S. & Guydosh, N. R. A cellular handbook for collided ribosomes: surveillance pathways and collision types. Curr. Genet. 67, 19–26 (2021).
Modrich, P. Mechanisms in E. coli and human mismatch repair (Nobel Lecture). Angew. Chem. Int. Ed. Engl. 55, 8490–8501 (2016).
Moore, S. D. & Sauer, R. T. The tmRNA system for translational surveillance and ribosome rescue. Annu. Rev. Biochem. 76, 101–124 (2007).
Joazeiro, C. A. P. Mechanisms and functions of ribosome-associated protein quality control. Nat. Rev. Mol. Cell Biol. 20, 368–383 (2019).
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).
Howard, C. J. & Frost, A. Ribosome-associated quality control and CAT tailing. Crit. Rev. Biochem. Mol. Biol. 56, 603–620 (2021).
Lytvynenko, I. et al. Alanine tails signal proteolysis in bacterial ribosome-associated quality control. Cell 178, 76–90 (2019).
D’Orazio, K. N. & Green, R. Ribosome states signal RNA quality control. Mol. Cell 81, 1372–1383 (2021).
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).
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).
Juszkiewicz, S. et al. ZNF598 is a quality control sensor of collided ribosomes. Mol. Cell 72, 469–481 (2018).
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).
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).
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).
Matsuo, Y. et al. RQT complex dissociates ribosomes collided on endogenous RQC substrate SDD1. Nat. Struct. Mol. Biol. 27, 323–332 (2020).
Matsuo, Y. et al. Ubiquitination of stalled ribosome triggers ribosome-associated quality control. Nat. Commun. 8, 159 (2017).
Glover, M. L. et al. NONU-1 encodes a conserved endonuclease required for mRNA translation surveillance. Cell Rep. 30, 4321–4331 (2020).
D’Orazio, K. N. et al. The endonuclease Cue2 cleaves mRNAs at stalled ribosomes during no go decay. eLife 8, e49117 (2019).
Nürenberg-Goloub, E. & Tampé, R. Ribosome recycling in mRNA translation, quality control, and homeostasis. Biol. Chem. 401, 47–61 (2019).
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).
Burby, P. E. & Simmons, L. A. MutS2 promotes homologous recombination in Bacillus subtilis. J. Bacteriol. 199, e00682-16 (2017).
Pinto, A. V. et al. Suppression of homologous and homeologous recombination by the bacterial MutS2 protein. Mol. Cell 17, 113–120 (2005).
Hingorani, M. M. Mismatch binding, ADP–ATP exchange and intramolecular signaling during mismatch repair. DNA Repair 38, 24–31 (2016).
Groothuizen, F. S. & Sixma, T. K. The conserved molecular machinery in DNA mismatch repair enzyme structures. DNA Repair 38, 14–23 (2016).
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).
Fukui, K. & Kuramitsu, S. Structure and function of the small MutS-related domain. Mol. Biol. Int. 2011, 691735 (2011).
Sachadyn, P. Conservation and diversity of MutS proteins. Mutat. Res. 694, 20–30 (2010).
Pochopien, A. A. et al. Structure of Gcn1 bound to stalled and colliding 80S ribosomes. Proc. Natl Acad. Sci. USA 118, e2022756118 (2021).
Sohmen, D. et al. Structure of the Bacillus subtilis 70S ribosome reveals the basis for species-specific stalling. Nat. Commun. 6, 6941 (2015).
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).
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).
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).
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).
Filbeck, S. et al. Mimicry of canonical translation elongation underlies alanine tail synthesis in RQC. Mol. Cell 81, 104–114 (2021).
Crowe-McAuliffe, C. et al. Structural basis for bacterial ribosome-associated quality control by RqcH and RqcP. Mol. Cell 81, 115–126 (2021).
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).
Thrun, A. et al. Convergence of mammalian RQC and C-end rule proteolytic pathways via alanine tailing. Mol. Cell 81, 2112–2122 (2021).
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).
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).
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).
Koo, B.-M. et al. Construction and analysis of two genome-scale deletion libraries for Bacillus subtilis. Cell Syst. 4, 291–305 (2017).
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).
Bucher, P., Karplus, K., Moeri, N. & Hofmann, K. A flexible motif search technique based on generalized profiles. Comput. Chem. 20, 3–23 (1996).
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).
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
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).
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
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).
Matzov, D. et al. The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus. Nat. Commun. 8, 723 (2017).
Hoffman, D. W. et al. Crystal structure of prokaryotic ribosomal protein L9: a bi-lobed RNA-binding protein. EMBO J. 13, 205–212 (1994).
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).
Liebschner, D. et al. Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Acta Crystallogr. D 75, 861–877 (2019).
Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D 66, 486–501 (2010).
Croll, T. I. ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps. Acta Crystallogr. D 74, 519–530 (2018).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
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).
Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996).
Ribeiro, J. V. et al. QwikMD—integrative molecular dynamics toolkit for novices and experts. Sci. Rep. 6, 26536 (2016).
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).
Phillips, J. C. et al. Scalable molecular dynamics on CPU and GPU architectures with NAMD. J. Chem. Phys. 153, 044130 (2020).
Rundlet, E. J. et al. Structural basis of early translocation events on the ribosome. Nature 595, 741–745 (2021).
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).
Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis. Protein Sci. 27, 14–25 (2018).
Amiri, H. & Noller, H. F. Structural evidence for product stabilization by the ribosomal mRNA helicase. RNA 25, 364–375 (2019).
More News
Author Correction: Bitter taste receptor activation by cholesterol and an intracellular tastant – Nature
Audio long read: How does ChatGPT ‘think’? Psychology and neuroscience crack open AI large language models
Ozempic keeps wowing: trial data show benefits for kidney disease