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Genetic and crystallographic approaches to investigating ribosome structure and function

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Ribosomes

Abstract

The past decade has seen tremendous advances in our understanding of the mechanism of protein synthesis, due in part to the solution of ribosome structures by X-ray crystallography. These structures have clarified our view of the decoding process so that it can now be understood in stereochemical terms, and have demonstrated that the ribosome is a ribozyme, catalyzing peptide bond formation using RNA’s capacity to adopt complex three-dimensional arrangements. While the ribosome structure solutions represent fundamental technical achievements, perhaps their most important contribution is that they explain some four decades of genetic and biochemical studies of the ribosome. It could perhaps be said with only slight exaggeration that little about the ribosome makes sense except in the light of its three-dimensional structure.

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References

  • Björkman J, Samuelsson P, Andersson DI, Hughes D (1999) Novel ribosomal mutations affecting translational accuracy, antibiotic resistance and virulence of Salmonella typhimurium. MolMicrobiol 31: 53–58

    Google Scholar 

  • Cameron DM, Gregory ST, Thompson J, Dahlberg AE (2004a) Thermus thermophilus L11 methyltransferase, PrmA, is dispensable for growth and preferentially modifies free ribosomal protein L11 prior to ribosome assembly. J Bacteriol 186: 5819–5825

    Article  PubMed  CAS  Google Scholar 

  • Cameron DM, Thompson J, Gregory ST, March PE, Dahlberg AE (2004b) Thiostrepton-resistant mutants of Thermus thermophilus. Nucleic Acids Res 32: 3220–3227

    Article  PubMed  CAS  Google Scholar 

  • Carr JF, Gregory ST, Dahlberg AE (2005) Severity of the streptomycin resistance and streptomycin dependence phenotypes of ribosomal protein S12 of Thermus thermophilus depends on the identity of highly conserved amino acid residues. J Bacteriol 187: 3548–3550

    Article  PubMed  CAS  Google Scholar 

  • Carter AP, Clemons WM, Brodersen DE, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V (2000) Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics. Nature 407: 340–348

    Article  PubMed  CAS  Google Scholar 

  • Cava F, Hidalgo, A, Berenguer J (2009) Thermus thermophilus as biological model. Extremophiles 13: 213–231

    Article  PubMed  CAS  Google Scholar 

  • Cochella L, Green R (2005) An active role for tRNA in decoding beyond codon:anticodon pairing. Science 308: 1178–1180

    Article  PubMed  CAS  Google Scholar 

  • Davis BD, Chen L, Tai PC (1986) Misread protein creates membrane channels: an essential step in the bactericidal action of aminoglycosides. Proc Natl Acad Sci USA 83: 6164–6168

    Article  PubMed  CAS  Google Scholar 

  • Demirci H, Belardinelli R, Seri E, Gregory ST, Gualerzi C, Dahlberg AE, Jogl G (2009) Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5′-methylthioadenosine. J Mol Biol 388: 271–282

    Article  PubMed  CAS  Google Scholar 

  • Duisterwinkel FJ, de Graaf JM, Kraal B, Bosch L (1981) A kirromycin resistant elongation factor EF-Tu from Escherichia coli contains a threonine instead of an alanine residue in position 375. FEBS Lett 131: 89–93

    Article  PubMed  CAS  Google Scholar 

  • Gale EF, Cundliffe E, Reynolds PE, Richmond MH, Waring MJ (1981) The molecular basis of antibiotic action. Wiley & Sons, London

    Google Scholar 

  • Gorini L, Rosset R, Zimmermann RA (1967) Phenotypic masking and streptomycin dependence. Science 157: 1314–1317

    Article  PubMed  CAS  Google Scholar 

  • Gregory ST, Cate JH, Dahlberg AE (2001a) A spontaneous, erythromycin-resistance mutation in a 23S rRNA gene, rrlA, of the extreme thermophile Thermus thermophilus. IB-21. J Bacteriol 183: 4382–4385

    Article  CAS  Google Scholar 

  • Gregory ST, Cate JH, Dahlberg AE (2001b) Streptomycin-resistant and streptomycin-dependent mutants of the extreme thermophile Thermus thermophilus. J Mol Biol 309: 333–338

    Article  PubMed  CAS  Google Scholar 

  • Gregory ST, Carr JF, Rodriguez-Correa D, Dahlberg AE (2005) Mutational analysis of 16S and 23S rRNA genes of Thermus thermophilus. J Bacteriol 187: 4804–4812

    Article  PubMed  CAS  Google Scholar 

  • Gregory ST, Dahlberg AE (2008) Transposition of an insertion sequence, ISTth7, in the genome of the extreme thermophile Thermus thermophilus HB8. FEMS Microbiol Lett 289: 187–192

    Article  PubMed  CAS  Google Scholar 

  • Gregory ST, Dahlberg AE (2009) Genetic and structural analysis of base substitutions in the central pseudoknot of Thermus thermophilus 16S ribosomal RNA. RNA 15: 215–223

    Article  PubMed  CAS  Google Scholar 

  • Gregory ST, Carr JF, Dahlberg AE (2009) A signal relay between ribosomal protein S12 and elongation factor EF-Tu during decoding of mRNA. RNA 15: 208–214

    Article  PubMed  CAS  Google Scholar 

  • Gromadski KB, Rodnina MV (2004) Streptomycin interferes with conformational coupling between codon recognition and GTPase activation on the ribosome. Nat Struct Mol Biol 11: 316–322

    Article  PubMed  CAS  Google Scholar 

  • Henne A, Brüggemann H, Raasch C, Wiezer A, Hartsch T, Liesegang H, Johann A, Lienard T, Gohl O, Martinez-Arias R, Jacobi C, Starkuviene V, Schlenczeck S, Dencker S, Huber R, Klenk HP, Kramer W, Merkl R, Gottschalk G, Fritz HJ (2004) The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol 22: 547–553

    Article  PubMed  CAS  Google Scholar 

  • Jawetz E, Gunnison JB, Bruff JB, Coleman VR (1952) Studies on antibiotic synergism and antagonism. Synergism among seven antibiotics against various bactera in vitro. J Bacteriol 64: 29–39

    CAS  Google Scholar 

  • Korostelev A, Noller HF (2007) The ribosome in focus: new structures bring new insights. Trends Biochem Sci 32: 434–441

    Article  PubMed  CAS  Google Scholar 

  • Lederberg J (1951) Streptomycin resistance; a genetically recessive mutation. J Bacteriol 61: 549–550

    PubMed  CAS  Google Scholar 

  • Masui R, Kurokawa K, Nakagawa N, Tokunaga F, Koyama Y, Shibata T, Oshima T, Yokoyama S, Yasunaga T, Kuramitsu S, NCBI (2005) Complete genome sequence of Thermus thermophilus HB8. http://www.ncbi.nlm.nih.gov/sites/entrez?db=genome&cmd=Retrieve&dopt=Overview&list_uids=530

  • Monshupanee T, Gregory ST, Douthwaite S, Chungjatupornchai W, Dahlberg AE (2008) Mutations in conserved helix 69 of 23S rRNA of Thermus thermophilus that affect capreomycin resistance but not posttranscriptional modifications. J Bacteriol 190: 7754–7761

    Article  PubMed  CAS  Google Scholar 

  • O’Connor M, Thomas CL, Zimmermann RA, Dahlberg AE (1997) Decoding fidelity at the ribosomal A and P sites: influence of mutations in three different regions of the decoding domain in 16S rRNA. Nucleic Acids Res 25: 1185–1193

    Article  CAS  Google Scholar 

  • Ogle JM, Brodersen DE, Clemons WM Jr, Tarry MJ, Carter AP, Ramakrishnan V (2001) Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 292: 897–902

    Article  PubMed  CAS  Google Scholar 

  • Ogle JM, Murphy FV, Tarry MJ, Ramakrishnan V (2002) Selection of tRNA by the ribosome requires a transition from an open to a closed form. Cell 111: 721–732

    Article  PubMed  CAS  Google Scholar 

  • Pfeiffer T, Jorcke D, Feltens R, Hartmann RK (1995) Direct linkage of str-, S10-and spc-related gene clusters in Thermus thermophilus HB8, and sequences of ribosomal proteins L4 and S10. Gene 167: 141–145

    Article  PubMed  CAS  Google Scholar 

  • Ramírez-Arcos S, Fernández-Herrero LA, Marín I, Berenguer J (1998) Anaerobic growth, a property horizontally transferred by an Hfr-like mechanism among extreme thermophiles. J Bacteriol 180: 3137–3143

    PubMed  Google Scholar 

  • Sakaki Y, Oshima T (1975) Isolation and characterization of a bacteriophage infectious to an extreme thermophile, Thermus thermophilus HB8. J Virol 15: 1449–1453

    PubMed  CAS  Google Scholar 

  • Schmeing TM, Ramakrishnan V (2009) What recent ribosome structures have revealed about the mechanism of translation. Nature 461: 1234–1242

    Article  PubMed  CAS  Google Scholar 

  • Schmeing TM, Voorhees RM, Kelley AC, Gao YG, Murphy FV 4th, Weir JR, Ramakrishnan V (2009) The crystal structure of the ribosome bound to EF-Tu and aminoacyl-tRNA. Science 326: 688–694

    Article  PubMed  CAS  Google Scholar 

  • Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH (2005) Structures of the bacterial ribosome at 3.5 Å resolution. Science 310: 827–834

    Article  PubMed  CAS  Google Scholar 

  • Timms AR, Bridges BA (1993) Double, independent mutational events in the rpsL gene of Escherichia coli: an example of hypermutability? Mol Microbiol 9: 335–342

    Article  PubMed  CAS  Google Scholar 

  • Tubulekas I, Buckingham RH, Hughes D (1991) Mutant ribosomes can generate dominant kirromycin resistance. J Bacteriol 173: 3635–3643

    PubMed  CAS  Google Scholar 

  • van Buul CP, Visser W, van Knippenberg PH (1984) Increased translational fidelity caused by the antibiotic kasugamycin and ribosomal ambiguity in mutants harbouring the ksgA gene. FEBS Lett 177: 119–124

    Article  Google Scholar 

  • Vila-Sanjurjo A, Ridgeway WK, Seymaner V, Zhang W, Santoso S, Yu K, Cate JH (2003) X-ray crystal structures of the WT and a hyper-accurate ribosome from Escherichia coli. Proc Natl Acad Sci USA 100: 8682–8687

    Article  PubMed  CAS  Google Scholar 

  • Vila-Sanjurjo A, Lu Y, Aragonez JL, Starkweather RE, Sasikumar M, O’Connor M (2007) Modulation of 16S rRNA function by ribosomal protein S12. Biochimica et Biophysica Acta 1769:462–471

    Article  PubMed  CAS  Google Scholar 

  • Xu Z, O’Farrell HC, Rife JP, Culver GM (2008) A conserved rRNA methyltransferase regulates ribosome biogenesis. Nat Struct Mol Biol 15: 534–536

    Article  PubMed  CAS  Google Scholar 

  • Yu MX, Slater MR, Ackermann HW (2006) Isolation and characterization of Thermus bacteriophages. Arch Virol 151: 663–679

    Article  PubMed  CAS  Google Scholar 

  • Zhang W, Dunkle JA, Cate JH (2009) Structures of the ribosome in intermediate states of ratcheting. Science 325: 1014–1017

    Article  PubMed  CAS  Google Scholar 

  • Zuurmond A-M, Zeef LAH, Kraal B (1998) A kirromycin-resistant EF-Tu species reverses streptomycin dependence of Escherichia coli strains mutated in ribosomal protein S12. Microbiol 144: 3309–3316

    Article  CAS  Google Scholar 

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Gregory, S.T. et al. (2011). Genetic and crystallographic approaches to investigating ribosome structure and function. In: Rodnina, M.V., Wintermeyer, W., Green, R. (eds) Ribosomes. Springer, Vienna. https://doi.org/10.1007/978-3-7091-0215-2_5

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