Warner, J. R. The economics of ribosome biosynthesis in yeast. Trends Biochem. Sci. 24, 437–440 (1999).
Google Scholar
Condon, C., Liveris, D., Squires, C., Schwartz, I. & Squires, C. L. rRNA operon multiplicity in Escherichia coli and the physiological implications of rrn inactivation. J. Bacteriol. 177, 4152–4156 (1995).
Google Scholar
Klappenbach, J. A., Dunbar, J. M. & Schmidt, T. M. rRNA operon copy number reflects ecological strategies of bacteria. Appl. Environ. Microbiol. 66, 1328–1333 (2000).
Google Scholar
Cheng, Z.-F. & Deutscher, M. P. Quality control of ribosomal RNA mediated by polynucleotide phosphorylase and RNase R. Proc. Natl Acad. Sci. USA 100, 6388–6393 (2003).
Google Scholar
Piir, K., Paier, A., Liiv, A., Tenson, T. & Maiväli, Ü. Ribosome degradation in growing bacteria. EMBO Rep. 12, 458–462 (2011).
Google Scholar
Roller, B. R. K., Stoddard, S. F. & Schmidt, T. M. Exploiting rRNA operon copy number to investigate bacterial reproductive strategies. Nat. Microbiol. 1, 16160 (2016).
Google Scholar
Bremer, H. & Dennis, P. P. Modulation of chemical composition and other parameters of the cell at different exponential growth rates. EcoSal Plus 3, ecosal.5.2.3 (2008).
Google Scholar
Li, S. H.-J. et al. Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions. Nat. Microbiol. 3, 939–947 (2018).
Google Scholar
Jacob, A. I., Köhrer, C., Davies, B. W., RajBhandary, U. L. & Walker, G. C. Conserved bacterial RNase YbeY plays key roles in 70S ribosome quality control and 16S rRNA maturation. Mol. Cell 49, 427–438 (2013).
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
Basturea, G. N., Zundel, M. A. & Deutscher, M. P. Degradation of ribosomal RNA during starvation: comparison to quality control during steady-state growth and a role for RNase PH. RNA 17, 338–345 (2011).
Google Scholar
Maiväli, Ü., Paier, A. & Tenson, T. When stable RNA becomes unstable: the degradation of ribosomes in bacteria and beyond. Biol. Chem. 394, 845–855 (2013).
Google Scholar
Smith, B. A., Gupta, N., Denny, K. & Culver, G. M. Characterization of 16S rRNA processing with pre-30S subunit assembly intermediates from E. coli. J. Mol. Biol. 430, 1745–1759 (2018).
Google Scholar
Sulthana, S. & Deutscher, M. P. Multiple exoribonucleases catalyze maturation of the 3′ terminus of 16S ribosomal RNA (rRNA). J. Biol. Chem. 288, 12574–12579 (2013).
Google Scholar
Arraiano, C. M., Matos, R. G. & Barbas, A. RNase II: the finer details of the Modus operandi of a molecular killer. RNA Biol. 7, 276–281 (2010).
Google Scholar
Lorentzen, E., Basquin, J., Tomecki, R., Dziembowski, A. & Conti, E. Structure of the active subunit of the yeast exosome core, Rrp44: diverse modes of substrate recruitment in the RNase II nuclease family. Mol. Cell 29, 717–728 (2008).
Google Scholar
Chen, C. & Deutscher, M. P. Elevation of RNase R in response to multiple stress conditions. J. Biol. Chem. 280, 34393–34396 (2005).
Google Scholar
Abula, A. et al. Molecular mechanism of RNase R substrate sensitivity for RNA ribose methylation. Nucleic Acids Res. 49, 4738–4749 (2021).
Google Scholar
Chu, L.-Y. et al. Structural insights into RNA unwinding and degradation by RNase R. Nucleic Acids Res. 45, 12015–12024 (2017).
Google Scholar
Chhabra, S., Mandell, Z. F., Liu, B., Babitzke, P. & Bechhofer, D. H. Analysis of mRNA decay intermediates in Bacillus subtilis 3′ exoribonuclease and RNA helicase mutant strains. mBio 13, e00400-22 (2022).
Google Scholar
Donovan, W. P. & Kushner, S. R. Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12. Proc. Natl Acad. Sci. USA 83, 120–124 (1986).
Google Scholar
Cheng, Z.-F., Zuo, Y., Li, Z., Rudd, K. E. & Deutscher, M. P. The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R. J. Biol. Chem. 273, 14077–14080 (1998).
Google Scholar
Kaplan, R. & Apirion, D. The involvement of ribonuclease I, ribonuclease II, and polynucleotide phosphorylase in the degradation of stable ribonucleic acid during carbon starvation in Escherichia coli. J. Biol. Chem. 249, 149–151 (1974).
Google Scholar
Sulthana, S., Basturea, G. N. & Deutscher, M. P. Elucidation of pathways of ribosomal RNA degradation: an essential role for RNase E. RNA 22, 1163–1171 (2016).
Google Scholar
Lipońska, A. & Yap, M.-N. F. Hibernation-promoting factor sequesters Staphylococcus aureus ribosomes to antagonize RNase R-mediated nucleolytic degradation. mBio 12, e0033421 (2021).
Google Scholar
Malecki, M., Bárria, C. & Arraiano, C. M. Characterization of the RNase R association with ribosomes. BMC Microbiol. 14, 34 (2014).
Google Scholar
Prossliner, T., Gerdes, K., Sørensen, M. A. & Winther, K. S. Hibernation factors directly block ribonucleases from entering the ribosome in response to starvation. Nucleic Acids Res. 49, 2226–2239 (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
Filbeck, S. et al. Mimicry of canonical translation elongation underlies alanine tail synthesis in RQC. Mol. Cell 81, 104–114 (2021).
Google Scholar
Frazão, C. et al. Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex. Nature 443, 110–114 (2006).
Google Scholar
Faehnle, C. R., Walleshauser, J. & Joshua-Tor, L. Mechanism of Dis3l2 substrate recognition in the Lin28–let-7 pathway. Nature 514, 252–256 (2014).
Google Scholar
Beckert, B. et al. Structure of a hibernating 100S ribosome reveals an inactive conformation of the ribosomal protein S1. Nat. Microbiol. 3, 1115–1121 (2018).
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
Boehringer, D., O’Farrell, H. C., Rife, J. P. & Ban, N. Structural insights into methyltransferase KsgA function in 30S ribosomal subunit biogenesis. J. Biol. Chem. 287, 10453–10459 (2012).
Google Scholar
Guo, Q. et al. Dissecting the in vivo assembly of the 30S ribosomal subunit reveals the role of RimM and general features of the assembly process. Nucleic Acids Res. 41, 2609–2620 (2013).
Google Scholar
Jahagirdar, D. et al. Alternative conformations and motions adopted by 30S ribosomal subunits visualized by cryo-electron microscopy. RNA 26, 2017–2030 (2020).
Google Scholar
Maksimova, E. M. et al. RbfA Is Involved in two important stages of 30S subunit assembly: formation of the central pseudoknot and docking of helix 44 to the decoding center. Int. J. Mol. Sci. 22, 6140 (2021).
Google Scholar
Maksimova, E., Kravchenko, O., Korepanov, A. & Stolboushkina, E. Protein assistants of small ribosomal subunit biogenesis in bacteria. Microorganisms 10, 747 (2022).
Google Scholar
Matos, R. G., Barbas, A. & Arraiano, C. M. RNase R mutants elucidate the catalysis of structured RNA: RNA-binding domains select the RNAs targeted for degradation. Biochem. J. 423, 291–301 (2009).
Google Scholar
Hossain, S. T., Malhotra, A. & Deutscher, M. P. The helicase activity of ribonuclease R Is essential for efficient nuclease activity. J. Biol. Chem. 290, 15697–15706 (2015).
Google Scholar
Hossain, S. T., Malhotra, A. & Deutscher, M. P. How RNase R degrades structured RNA: role of the helicase activity and the S1 domain. J. Biol. Chem. 291, 7877–7887 (2016).
Google Scholar
Loh, P. C., Morimoto, T., Matsuo, Y., Oshima, T. & Ogasawara, N. The GTP-binding protein YqeH participates in biogenesis of the 30S ribosome subunit in Bacillus subtilis. Genes Genet. Syst. 82, 281–289 (2007).
Google Scholar
Nishima, W. et al. Hyper-swivel head domain motions are required for complete mRNA–tRNA translocation and ribosome resetting. Nucleic Acids Res. 50, 8302–8320 (2022).
Google Scholar
Li, Z. RNA quality control: degradation of defective transfer RNA. EMBO J. 21, 1132–1138 (2002).
Google Scholar
Bralley, P., Gust, B., Chang, S., Chater, K. F. & Jones, G. H. RNA 3′-tail synthesis in Streptomyces: in vitro and in vivo activities of RNase PH, the SCO3896 gene product and polynucleotide phosphorylase. Microbiology 152, 627–636 (2006).
Google Scholar
Mohanty, B. K. & Kushner, S. R. Analysis of the function of Escherichia coli poly(A) polymerase I in RNA metabolism. Mol. Microbiol. 34, 1094–1108 (1999).
Google Scholar
Campos-Guillén, J., Bralley, P., Jones, G. H., Bechhofer, D. H. & Olmedo-Alvarez, G. Addition of poly(A) and heteropolymeric 3′ ends in Bacillus subtilis wild-type and polynucleotide phosphorylase-deficient strains. J. Bacteriol. 187, 4698–4706 (2005).
Google Scholar
Hussain, T., Llácer, J. L., Wimberly, B. T., Kieft, J. S. & Ramakrishnan, V. Large-scale movements of IF3 and tRNA during bacterial translation initiation. Cell 167, 133–144 (2016).
Google Scholar
Failmezger, J., Nitschel, R., Sánchez-Kopper, A., Kraml, M. & Siemann-Herzberg, M. Site-specific cleavage of ribosomal RNA in Escherichia coli-based cell-free protein synthesis systems. PLoS ONE 11, e0168764 (2016).
Google Scholar
Schedlbauer, A. et al. A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit. Sci. Adv. 7, eabf7547 (2021).
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).
Google Scholar
Franken, L. E. et al. A general mechanism of ribosome dimerization revealed by single-particle cryo-electron microscopy. Nat. Commun. 8, 722 (2017).
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
Khusainov, I. et al. Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF. EMBO J. 36, 2073–2087 (2017).
Google Scholar
Cerullo, F. et al. Bacterial ribosome collision sensing by a MutS DNA repair ATPase paralogue. Nature 603, 509–514 (2022).
Google Scholar
Sambrook, J., Fritsch, E. F. & Maniatis, T. Molecular Cloning: A Laboratory Manual 2nd edn (Cold Spring Harbor Laboratory Press, 1989).
Liu, H. & Naismith, J. H. An efficient one-step site-directed deletion, insertion, single and multiple-site plasmid mutagenesis protocol. BMC Biotechnol. 8, 91 (2008).
Google Scholar
Dimitrova, L. et al. Structural characterization of the Chaetomium thermophilum TREX-2 complex and its interaction with the mRNA nuclear export factor Mex67:Mtr2. Structure 23, 1246–1257 (2015).
Google Scholar
Blaha, G. et al. in Methods in Enzymology Vol. 317 (eds. Abelson, J. N. & Celander, D. W.) 292–309 (Elsevier, 2000).
Arenz, S. et al. Drug sensing by the ribosome induces translational arrest via active site perturbation. Mol. Cell 56, 446–452 (2014).
Google Scholar
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).
Google Scholar
Zivanov, J., Nakane, T. & Scheres, S. H. W. A Bayesian approach to beam-induced motion correction in cryo-EM single-particle analysis. IUCrJ 6, 5–17 (2019).
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).
Google Scholar
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
Google Scholar
Wagner, T. et al. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun. Biol. 2, 218 (2019).
Google Scholar
Wagner, T. & Raunser, S. The evolution of SPHIRE-crYOLO particle picking and its application in automated cryo-EM processing workflows. Commun. Biol. 3, 61 (2020).
Google Scholar
Casañal, A., Lohkamp, B. & Emsley, P. Current developments in Coot for macromolecular model building of electron cryo‐microscopy and crystallographic data. Protein Sci. 29, 1055–1064 (2020).
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
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Google Scholar
Kovalevskiy, O., Nicholls, R. A., Long, F., Carlon, A. & Murshudov, G. N. Overview of refinement procedures within REFMAC 5: utilizing data from different sources. Acta Crystallogr. D 74, 215–227 (2018).
Google Scholar
Nicholls, R. A., Fischer, M., McNicholas, S. & Murshudov, G. N. Conformation-independent structural comparison of macromolecules with ProSMART. Acta Crystallogr. D 70, 2487–2499 (2014).
Google Scholar
Varadi, M. et al. AlphaFold protein structure database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 50, D439–D444 (2022).
Google Scholar
Goddard, T. D. et al. UCSF ChimeraX: meeting modern challenges in visualization and analysis: UCSF ChimeraX Visualization System. Protein Sci. 27, 14–25 (2018).
Google Scholar
Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021).
Google Scholar
Yamashita, K., Palmer, C. M., Burnley, T. & Murshudov, G. N. Cryo-EM single-particle structure refinement and map calculation using Servalcat. Acta Crystallogr. D 77, 1282–1291 (2021).
Google Scholar
Sweeney, B. A. et al. R2DT is a framework for predicting and visualising RNA secondary structure using templates. Nat. Commun. 12, 3494 (2021).
Google Scholar
Pedreira, T., Elfmann, C. & Stülke, J. The current state of SubtiWiki, the database for the model organism Bacillus subtilis. Nucleic Acids Res. 50, D875–D882 (2022).
Google Scholar
Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).