Structural basis for aminoglycoside inhibition of bacterial ribosome recycling (original) (raw)

• Magnet, S. & Blanchard, J.S. Molecular insights into aminoglycoside action and resistance. Chem. Rev. 105, 477–498 (2005).
  Article CAS Google Scholar
• Sutcliffe, J.A. Improving on nature: antibiotics that target the ribosome. Curr. Opin. Microbiol. 8, 534–542 (2005).
  Article CAS Google Scholar
• Davies, J., Gorini, L. & Davies, B.D. Misreading of RNA codewords induced by aminoglycoside antibiotics. Mol. Pharmacol. 1, 93–106 (1965).
  CAS Google Scholar
• Davies, J., Jones, D.S. & Khorana, H.G. A further study of misreading of codons induced by streptomycin and neomycin using ribopolynucleotides containing two nucleotides in alternating sequence as templates. J. Mol. Biol. 18, 48–57 (1966).
  Article CAS Google Scholar
• Cabañas, M.J., Vázquez, D. & Modolell, J. Inhibition of ribosomal translocation by aminoglycoside antibiotics. Biochem. Biophys. Res. Commun. 83, 991–997 (1978).
  Article Google Scholar
• Misumi, M., Nishimura, T., Komai, T. & Tanaka, N. Interaction of kanamycin and related antibiotics with the large subunit of ribosomes and the inhibition of translocation. Biochem. Biophys. Res. Commun. 84, 358–365 (1978).
  Article CAS Google Scholar
• Hirokawa, G. et al. Post-termination complex disassembly by ribosome recycling factor, a functional tRNA mimic. EMBO J. 21, 2272–2281 (2002).
  Article CAS PubMed Google Scholar
• Wilson, D.N. & Nierhaus, K.H. The how and Y of cold shock. Nat. Struct. Mol. Biol. 11, 1026–1028 (2004).
  Article CAS Google Scholar
• Janosi, L. et al. Evidence for in vivo ribosome recycling, the fourth step in protein biosynthesis. EMBO J. 17, 1141–1151 (1998).
  Article CAS PubMed Google Scholar
• Zavialov, A.V., Hauryliuk, V.V. & Ehrenberg, M. Splitting of the posttermination ribosome into subunits by the concerted action of RRF and EF-G. Mol. Cell 18, 675–686 (2005).
  Article CAS Google Scholar
• Gao, N. et al. Mechanism for the disassembly of the posttermination complex inferred from cryo-EM studies. Mol. Cell 18, 663–674 (2005).
  Article CAS PubMed Google Scholar
• Peske, F., Rodnina, M.V. & Wintermeyer, W. Sequence of steps in ribosome recycling as defined by kinetic analysis. Mol. Cell 18, 403–412 (2005).
  Article CAS Google Scholar
• Hirokawa, G., Demeshkina, N., Iwakura, N., Kaji, H. & Kaji, A. The ribosome-recycling step: consensus or controversy? Trends Biochem. Sci. 31, 143–149 (2006).
  Article CAS Google Scholar
• Hirokawa, G. et al. The role of ribosome recycling factor in dissociation of 70S ribosomes into subunits. RNA 11, 1317–1328 (2005).
  Article CAS PubMed Google Scholar
• Teyssier, E. et al. Temperature-sensitive mutation in yeast mitochondrial ribosome-recycling factor (RRF). Nucleic Acids Res. 31, 4218–4226 (2003).
  Article CAS PubMed Google Scholar
• Rolland, N. et al. Plant ribosome recycling factor homologue is a chloroplastic protein and is bactericidal in Escherichia coli carrying temperature-sensitive ribosome recycling factor. Proc. Natl. Acad. Sci. USA 96, 5464–5469 (1999).
  Article CAS Google Scholar
• Janosi, L., Shimizu, I. & Kaji, A. Ribosome recycling factor (ribosome releasing factor) is essential for bacterial growth. Proc. Natl. Acad. Sci. USA 91, 4249–4253 (1994).
  Article CAS PubMed Google Scholar
• Campuzano, S., Vázquez, D. & Modolell, J. Functional interaction of neomycin B and related antibiotics with 30S and 50S ribosomal subunits. Biochem. Biophys. Res. Commun. 87, 960–966 (1979).
  Article CAS Google Scholar
• Carter, A.P. et al. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407, 340–348 (2000).
  Article CAS Google Scholar
• Selmer, M. et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313, 1935–1942 (2006).
  Article CAS Google Scholar
• Schuwirth, B.S. et al. Structures of the bacterial ribosome at 3.5 Å resolution. Science 310, 827–834 (2005).
  Article CAS Google Scholar
• Moazed, D. & Noller, H.F. Interaction of antibiotics with functional sites in 16S ribosomal RNA. Nature 327, 389–394 (1987).
  Article CAS Google Scholar
• Yusupov, M.M. et al. Crystal structure of the ribosome at 5.5 Å resolution. Science 292, 883–896 (2001).
  Article CAS Google Scholar
• Cannone, J.J. et al. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3, 2 (2002).
  Article PubMed Google Scholar
• Lancaster, L., Kiel, M.C., Kaji, A. & Noller, H.F. Orientation of ribosome recycling factor in the ribosome from directed hydroxyl radical probing. Cell 111, 129–140 (2002).
  Article CAS PubMed Google Scholar
• Valle, M. et al. Locking and unlocking of ribosomal motions. Cell 114, 123–134 (2003).
  Article CAS Google Scholar
• Agrawal, R.K. et al. Visualization of ribosome-recycling factor on the Escherichia coli 70S ribosome: functional implications. Proc. Natl. Acad. Sci. USA 101, 8900–8905 (2004).
  Article CAS PubMed Google Scholar
• Connell, S.R. et al. Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors. Mol. Cell 25, 751–764 (2007).
  Article CAS Google Scholar
• Raj, V.S., Kaji, H. & Kaji, A. Interaction of RRF and EF-G from E. coli and T. thermophilus with ribosomes from both origins—insight into the mechanism of the ribosome recycling step. RNA 11, 275–284 (2005).
  Article CAS PubMed Google Scholar
• Wilson, D.N. et al. X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit. EMBO J. 24, 251–260 (2005).
  Article CAS PubMed Google Scholar
• Ali, I.K., Lancaster, L., Feinberg, J., Joseph, S. & Noller, H.F. Deletion of a conserved, central ribosomal intersubunit RNA bridge. Mol. Cell 23, 865–874 (2006).
  Article CAS Google Scholar
• Liiv, A., Karitkina, D., Maiväli, U. & Remme, J. Analysis of the function of E. coli 23S rRNA helix-loop 69 by mutagenesis. BMC Mol. Biol. 6, 18 (2005).
  Article PubMed Google Scholar
• Rackham, O., Wang, K. & Chin, J.W. Functional epitopes at the ribosome subunit interface. Nat. Chem. Biol. 2, 254–258 (2006).
  Article CAS Google Scholar
• Frank, J. & Agrawal, R.K. A ratchet-like intersubunit reorganization of the ribosome during translocation. Nature 406, 318–322 (2000).
  Article CAS Google Scholar
• Horan, L.H. & Noller, H.F. Intersubunit movement is required for ribosomal translocation. Proc. Natl. Acad. Sci. USA 104, 4881–4885 (2007).
  Article CAS Google Scholar
• Campuzano, S., Vázquez, D. & Modolell, J. Dissociation of guanosine nucleotide-elongation factor G-ribosome complexes. Biochemistry 18, 1570–1574 (1979).
  Article CAS Google Scholar
• Senior, K. Duchenne muscular dystrophy improved by gentamicin. Mol. Med. Today 5, 461 (1999).
  Article CAS Google Scholar
• Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).
  Article CAS PubMed Google Scholar
• Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994).
• Brünger, A.T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905–921 (1998).
  Article PubMed Google Scholar
• Yoshizawa, S., Fourmy, D. & Puglisi, J.D. Structural origins of gentamicin antibiotic action. EMBO J. 17, 6437–6448 (1998).
  Article CAS PubMed Google Scholar
• Cowtan, K. General quadratic functions in real and reciprocal space and their application to likelihood phasing. Acta Crystallogr. D Biol. Crystallogr. 56, 1612–1621 (2000).
  Article CAS Google Scholar
• Kleywegt, G.J. & Jones, T.A. Databases in protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 54, 1119–1131 (1998).
  Article CAS Google Scholar
• Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991).
  Article PubMed Google Scholar
• Toyoda, T. et al. Crystal structure combined with genetic analysis of the Thermus thermophilus ribosome recycling factor shows that a flexible hinge may act as a functional switch. RNA 6, 1432–1444 (2000).
  Article CAS PubMed Google Scholar
• Carson, M. Ribbons. Methods Enzymol. 277, 493–502 (1997).
  Article CAS Google Scholar