Context-Specific Action of Ribosomal Antibiotics

Literature Cited

1. 1.  Almutairi MM, Svetlov MS, Hansen DA, Khabibullina NF, Klepacki D et al. 2017. Co-produced natural ketolides methymycin and pikromycin inhibit bacterial growth by preventing synthesis of a limited number of proteins. Nucleic Acids Res 45:9573–82
   [Google Scholar]
2. 2.  Alvarez-Elcoro S, Enzler MJ 1999. The macrolides: erythromycin, clarithromycin, and azithromycin. Mayo Clin. Proc. 74:613–34
   [Google Scholar]
3. 3.  Anderson KM, Castelli WP, Levy D 1987. Cholesterol and mortality: 30 years of follow-up from the Framingham study. JAMA 257:2176–80
   [Google Scholar]
4. 4.  Arenz S, Bock LV, Graf M, Innis CA, Beckmann R et al. 2016. A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest. Nat. Commun. 7:12026
   [Google Scholar]
5. 5.  Arenz S, Juette MF, Graf M, Nguyen F, Huter P et al. 2016. Structures of the orthosomycin antibiotics avilamycin and evernimicin in complex with the bacterial 70S ribosome. PNAS 113:7527–32
   [Google Scholar]
6. 6.  Arenz S, Meydan S, Starosta A, Berninghausen O, Beckmann R et al. 2014. Drug sensing by the ribosome induces translational arrest via active site perturbation. Mol. Cell 56:446–52
   [Google Scholar]
7. 7.  Arenz S, Ramu H, Gupta P, Berninghausen O, Beckmann R et al. 2014. Molecular basis for erythromycin-dependent ribosome stalling during translation of the ErmBL leader peptide. Nat. Commun. 5:3501
   [Google Scholar]
8. 8.  Balakin AG, Skripkin EA, Shatsky IN, Bogdanov AA 1992. Unusual ribosome binding properties of mRNA encoding bacteriophage λ repressor. Nucleic Acids Res 20:563–71
   [Google Scholar]
9. 9.  Belousoff MJ, Eyal Z, Radjainia M, Ahmed T, Bamert RS et al. 2017. Structural basis for linezolid binding site rearrangement in the Staphylococcus aureus ribosome. mBio 8:e00395–17
   [Google Scholar]
10. 10.  Brodersen DE, Clemons WM Jr., Carter AP, Morgan-Warren RJ, Wimberly BT, Ramakrishnan V 2000. The structural basis for the action of the antibiotics tetracycline, pactamycin, and hygromycin B on the 30S ribosomal subunit. Cell 103:1143–54
    [Google Scholar]
11. 11.  Bryskier A, Denis A 2002. Ketolides: novel antibacterial agents designed to overcome resistance to erythromycin A within gram-positive cocci. Macrolide Antibiotics W Schönfeld, HA Kirst 97–140 Basel: Birkhäuser Verlag
    [Google Scholar]
12. 12.  Bulkley D, Innis CA, Blaha G, Steitz TA 2010. Revisiting the structures of several antibiotics bound to the bacterial ribosome. PNAS 107:17158–63
    [Google Scholar]
13. 13.  Cannon M 1968. The puromycin reaction and its inhibition by chloramphenicol. Eur. J. Biochem. 7:137–45
    [Google Scholar]
14. 14.  Chen J, Choi J, O'Leary SE, Prabhakar A, Petrov A et al. 2016. The molecular choreography of protein synthesis: translational control, regulation, and pathways. Q. Rev. Biophys. 49:e11
    [Google Scholar]
15. 15.  Chin K, Shean CS, Gottesman ME 1993. Resistance of λcI translation to antibiotics that inhibit translation initiation. J. Bacteriol. 175:7471–73First evidence that kasugamycin differentially inhibits translation depending on the structure of mRNA.
    [Google Scholar]
16. 16.  Cochella L, Green R 2005. An active role for tRNA in decoding beyond codon:anticodon pairing. Science 308:1178–80
    [Google Scholar]
17. 17.  Dadu RT, Ballantyne CM 2014. Lipid lowering with PCSK9 inhibitors. Nat. Rev. Cardiol. 11:563–75
    [Google Scholar]
18. 18.  Dale T, Uhlenbeck OC 2005. Amino acid specificity in translation. Trends Biochem. Sci. 30:659–65
    [Google Scholar]
19. 19.  Davies J, Spiegelman GB, Yim G 2006. The world of subinhibitory antibiotic concentrations. Curr. Opin. Microbiol. 9:445–53
    [Google Scholar]
20. 20.  Davis AR, Gohara DW, Yap MN 2014. Sequence selectivity of macrolide-induced translational attenuation. PNAS 111:15379–84One of the first two papers reporting that macrolides act as context-specific antibiotics in vivo.
    [Google Scholar]
21. 21.  Dinos G, Wilson DN, Teraoka Y, Szaflarski W, Fucini P et al. 2004. Dissecting the ribosomal inhibition mechanisms of edeine and pactamycin: the universally conserved residues G693 and C795 regulate P-site RNA binding. Mol. Cell 13:113–24First evidence that the action of pactamycin may depend on the nature of the A site substrate.
    [Google Scholar]
22. 22.  Dinos GP 2017. The macrolide antibiotic renaissance. Br. J. Pharmacol. 174:2967–83
    [Google Scholar]
23. 23.  Dorner S, Brunelle JL, Sharma D, Green R 2006. The hybrid state of tRNA binding is an authentic translation elongation intermediate. Nat. Struct. Mol. Biol. 13:234–41
    [Google Scholar]
24. 24.  Dunkle JA, Xiong L, Mankin AS, Cate JH 2010. Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action. PNAS 107:17152–57
    [Google Scholar]
25. 25.  Egebjerg J, Garrett RA 1991. Binding sites of the antibiotics pactamycin and celesticetin on ribosomal RNAs. Biochimie 73:1145–49
    [Google Scholar]
26. 26.  Erlacher MD, Lang K, Shankaran N, Wotzel B, Huttenhofer A et al. 2005. Chemical engineering of the peptidyl transferase center reveals an important role of the 2′-hydroxyl group of A2451. Nucleic Acids Res 33:1618–27
    [Google Scholar]
27. 27.  Fahlman RP, Dale T, Uhlenbeck OC 2004. Uniform binding of aminoacylated transfer RNAs to the ribosomal A and P sites. Mol. Cell 16:799–805
    [Google Scholar]
28. 28.  Fei J, Richard AC, Bronson JE, Gonzalez RL Jr. 2011. Transfer RNA-mediated regulation of ribosome dynamics during protein synthesis. Nat. Struct. Mol. Biol. 18:1043–51
    [Google Scholar]
29. 29.  Fernandes P 2015. Use of antibiotic core structures to generate new and useful macrolide antibiotics. Antibiotics: Current Innovations and Future Trends S Sánchez, AL Demain 375–93 Norfolk, UK: Caister Acad.
    [Google Scholar]
30. 30.  Gale EF, Cundliffe E, Reynolds PE, Richmond MH, Waring MJ 1981. The Molecular Basis of Antibiotic Action London: John Wiley
31. 31.  Gottesman ME 1967. Reaction of ribosome-bound peptidyl transfer ribonucleic acid with aminoacyl transfer ribonucleic acid or puromycin. J. Biol. Chem. 242:5564–71
    [Google Scholar]
32. 32.  Gupta P, Liu B, Klepacki D, Gupta V, Schulten K et al. 2016. Nascent peptide assists the ribosome in recognizing chemically distinct small molecules. Nat. Chem. Biol. 12:153–58
    [Google Scholar]
33. 33.  Hartz D, McPheeters DS, Traut R, Gold L 1988. Extension inhibition analysis of translation initiation complexes. Methods Enzymol 164:419–25Introduction of toeprinting analysis, one of the methodologies that can reveal context specificity of ribosomal inhibitors.
    [Google Scholar]
34. 34.  Hirashima A, Childs G, Inouye M 1973. Differential inhibitory effects of antibiotics on the biosynthesis of envelope proteins of Escherichia coli. J. Mol. . Biol 79:373–89
    [Google Scholar]
35. 35.  Horinouchi S, Weisblum B 1980. Posttranscriptional modification of mRNA conformation: mechanism that regulates erythromycin-induced resistance. PNAS 77:7079–83
    [Google Scholar]
36. 36.  Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218–23Introduction of Ribo-seq, an approach able to reveal context-specific action of antibiotics in vivo.
    [Google Scholar]
37. 37.  Ippolito JA, Kanyo ZF, Wang D, Franceschi FJ, Moore PB et al. 2008. Crystal structure of the oxazolidinone antibiotic linezolid bound to the 50S ribosomal subunit. J. Med. Chem. 51:3353–56
    [Google Scholar]
38. 38.  Johansson M, Chen J, Tsai A, Kornberg G, Puglisi JD 2014. Sequence-dependent elongation dynamics on macrolide-bound ribosomes. Cell Rep 7:1534–46
    [Google Scholar]
39. 39.  Johansson M, Ieong KW, Trobro S, Strazewski P, Aqvist J et al. 2011. pH-sensitivity of the ribosomal peptidyl transfer reaction dependent on the identity of the A-site aminoacyl-tRNA. PNAS 108:79–84
    [Google Scholar]
40. 40.  Kaberdina AC, Szaflarski W, Nierhaus KH, Moll I 2009. An unexpected type of ribosomes induced by kasugamycin: a look into ancestral times of protein synthesis?. Mol. Cell 33:227–36Report that kasugamycin induces formation of specialized ribosomes that preferentially translate a subset of proteins.
    [Google Scholar]
41. 41.  Kannan K, Kanabar P, Schryer D, Florin T, Oh E et al. 2014. The general mode of translation inhibition by macrolide antibiotics. PNAS 111:15958–63Along with Reference 20, first evidence of the context specificity of macrolide antibiotics action in vivo.
    [Google Scholar]
42. 42.  Kannan K, Vázquez-Laslop N, Mankin AS 2012. Selective protein synthesis by ribosomes with a drug-obstructed exit tunnel. Cell 151:508–20
    [Google Scholar]
43. 43.  Kloss P, Xiong L, Shinabarger DL, Mankin AS 1999. Resistance mutations in 23S rRNA identify the site of action of protein synthesis inhibitor, linezolid, in the ribosomal peptidyl transferase center. J. Mol. Biol. 294:93–101
    [Google Scholar]
44. 44.  Konevega AL, Fischer N, Semenkov YP, Stark H, Wintermeyer W, Rodnina MV 2007. Spontaneous reverse movement of mRNA-bound tRNA through the ribosome. Nat. Struct. Mol. Biol. 14:318–24
    [Google Scholar]
45. 45.  Kozak M, Nathans D 1972. Differential inhibition of coliphage MS2 protein synthesis by ribosome-directed antibiotics. J. Mol. Biol. 70:41–55
    [Google Scholar]
46. 46.  Leach KL, Swaney SM, Colca JR, McDonald WG, Blinn JR et al. 2007. The site of action of oxazolidinone antibiotics in living bacteria and in human mitochondria. Mol. Cell 26:393–402
    [Google Scholar]
47. 47.  Lintner NG, McClure KF, Petersen D, Londregan AT, Piotrowski DW et al. 2017. Selective stalling of human translation through small-molecule engagement of the ribosome nascent chain. PLOS Biol 15:e2001882Description of a ribosomal inhibitor that specifically arrests translation of a handful of human proteins.
    [Google Scholar]
48. 48.  Lovett PS 1996. Translation attenuation regulation of chloramphenicol resistance in bacteria—A review. Gene 179:157–62
    [Google Scholar]
49. 49.  Lovmar M, Nilsson K, Vimberg V, Tenson T, Nervall M, Ehrenberg M 2006. The molecular mechanism of peptide-mediated erythromycin resistance. J. Biol. Chem. 281:6742–50
    [Google Scholar]
50. 50.  Mankin AS 1997. Pactamycin resistance mutations in functional sites of 16S rRNA. J. Mol. Biol. 274:8–15
    [Google Scholar]
51. 51.  Marks J, Kannan K, Roncase EJ, Klepacki D, Kefi A et al. 2016. Context-specific inhibition of translation by ribosomal antibiotics targeting the peptidyl transferase center. PNAS 113:12150–55Demonstration that the action of PTC inhibitors chloramphenicol and linezolid is context specific.
    [Google Scholar]
52. 52.  Moellering RC 2003. Linezolid: the first oxazolidinone antimicrobial. Ann. Intern. Med. 138:135–42
    [Google Scholar]
53. 53.  Moll I, Blasi U 2002. Differential inhibition of 30S and 70S translation initiation complexes on leaderless mRNA by kasugamycin. Biochem. Biophys. Res. Commun. 297:1021–26
    [Google Scholar]
54. 54.  Moll I, Hirokawa G, Kiel MC, Kaji A, Blasi U 2004. Translation initiation with 70S ribosomes: an alternative pathway for leaderless mRNAs. Nucleic Acids Res 32:3354–63
    [Google Scholar]
55. 55.  Monro RE, Vazquez D 1967. Ribosome-catalysed peptidyl transfer: effects of some inhibitors of protein synthesis. J. Mol. Biol. 28:161–65
    [Google Scholar]
56. 56.  Muto H, Nakatogawa H, Ito K 2006. Genetically encoded but nonpolypeptide prolyl-tRNA functions in the A site for SecM-mediated ribosomal stall. Mol. Cell 22:545–52
    [Google Scholar]
57. 57.  Nakahigashi K, Takai Y, Shiwa Y, Wada M, Honma M et al. 2014. Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo. BMC Genom 15:1115
    [Google Scholar]
58. 58.  Odom OW, Picking WD, Tsalkova T, Hardesty B 1991. The synthesis of polyphenylalanine on ribosomes to which erythromycin is bound. Eur. J. Biochem. 198:713–22
    [Google Scholar]
59. 59.  Oh E, Becker AH, Sandikci A, Huber D, Chaba R et al. 2011. Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Cell 147:1295–308
    [Google Scholar]
60. 60.  Okuyama A, Machiyama N, Kinoshita T, Tanaka N 1971. Inhibition by kasugamycin of initiation complex formation on 30S ribosomes. Biochem. Biophys. Res. Commun. 43:196–99
    [Google Scholar]
61. 61.  Okuyama A, Tanaka N 1972. Differential effects of aminoglycosides on cistron-specific initiation of protein synthesis. Biochem. Biophys. Res. Commun. 49:951–57
    [Google Scholar]
62. 62.  Orelle C, Carlson S, Kaushal B, Almutairi MM, Liu H et al. 2013. Tools for characterizing bacterial protein synthesis inhibitors. Antimicrob. Agents Chemother. 57:5994–6004
    [Google Scholar]
63. 63.  Otaka T, Kaji A 1975. Release of (oligo) peptidyl-tRNA from ribosomes by erythromycin A. PNAS 72:2649–52
    [Google Scholar]
64. 64.  Pantel L, Florin T, Dobosz-Bartoszek M, Racine E, Sarciaux M et al. 2018. Odilorhabdins, antibacterial agents that cause miscoding by binding at a new ribosomal site. Mol. Cell 70:83–94.e7
    [Google Scholar]
65. 65.  Patel U, Yan YP, Hobbs FW Jr., Kaczmarczyk J, Slee AM et al. 2001. Oxazolidinones mechanism of action: inhibition of the first peptide bond formation. J. Biol. Chem. 276:37199–205
    [Google Scholar]
66. 66.  Pestka S 1972. Studies on transfer ribonucleic acid-ribosome complexes: XIX. Effect of antibiotics on peptidyl puromycin synthesis on polyribosomes from Escherichia coli. J. Biol. . Chem 247:4669–78
    [Google Scholar]
67. 67.  Pestka S 1975. Chloramphenicol. Mechanism of Action of Antimicrobial and Antitumor Agents JW Corcoran, FE Hahn 370–95 Antibiotics , Vol. 3 Berlin: Springer-Verlag
    [Google Scholar]
68. 68.  Petersen DN, Hawkins J, Ruangsiriluk W, Stevens KA, Maguire BA et al. 2016. A small-molecule anti-secretagogue of PCSK9 targets the 80S ribosome to inhibit PCSK9 protein translation. Chem. Biol. 23:1362–71
    [Google Scholar]
69. 69.  Polacek N, Gaynor M, Yassin A, Mankin AS 2001. Ribosomal peptidyl transferase can withstand mutations at the putative catalytic nucleotide. Nature 411:498–501
    [Google Scholar]
70. 70.  Polacek N, Mankin AS 2005. The ribosomal peptidyl transferase center: structure, function, evolution, inhibition. Crit. Rev. Biochem. Mol. Biol. 40:285–311
    [Google Scholar]
71. 71.  Poldermans B, Van Buul CP, Van Knippenberg PH 1979. Studies on the function of two adjacent N6,N6-dimethyladenosines near the 3′ end of 16 S ribosomal RNA of Escherichia coli: II. The effect of the absence of the methyl groups on initiation of protein biosynthesis. J. Biol. Chem. 254:9090–93
    [Google Scholar]
72. 72.  Polikanov YS, Osterman IA, Szal T, Tashlitsky VN, Serebryakova MV et al. 2014. Amicoumacin A inhibits translation by stabilizing mRNA interaction with the ribosome. Mol. Cell 56:531–40
    [Google Scholar]
73. 73.  Polikanov YS, Starosta AL, Juette MF, Altman RB, Terry DS et al. 2015. Distinct tRNA accommodation intermediates observed on the ribosome with the antibiotics hygromycin A and A201A. Mol. Cell 58:832–44
    [Google Scholar]
74. 74.  Polikanov YS, Steitz TA, Innis CA 2014. A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome. Nat. Struct. Mol. Biol. 21:787–93
    [Google Scholar]
75. 75.  Polikanov YS, Szal T, Jiang F, Gupta P, Matsuda R et al. 2014. Negamycin interferes with decoding and translocation by simultaneous interaction with rRNA and tRNA. Mol. Cell 56:541–50
    [Google Scholar]
76. 76.  Ramu H, Mankin A, Vázquez-Laslop N 2009. Programmed drug-dependent ribosome stalling. Mol. Microbiol. 71:811–24
    [Google Scholar]
77. 77.  Ramu H, Vázquez-Laslop N, Klepacki D, Dai Q, Piccirilli J et al. 2011. Nascent peptide in the ribosome exit tunnel affects functional properties of the A-site of the peptidyl transferase center. Mol. Cell 41:321–30
    [Google Scholar]
78. 78.  Ranjan N, Rodnina MV 2017. Thio-modification of tRNA at the wobble position as regulator of the kinetics of decoding and translocation on the ribosome. J. Am. Chem. Soc. 139:5857–64
    [Google Scholar]
79. 79.  Rosenblum G, Chen C, Kaur J, Cui X, Zhang H et al. 2013. Quantifying elongation rhythm during full-length protein synthesis. J. Am. Chem. Soc. 135:11322–29
    [Google Scholar]
80. 80.  Schluenzen F, Takemoto C, Wilson DN, Kaminishi T, Harms JM et al. 2006. The antibiotic kasugamycin mimics mRNA nucleotides to destabilize tRNA binding and inhibit canonical translation initiation. Nat. Struct. Mol. Biol. 13:871–78 Erratum. 2006 Nat. Struct. Mol. Biol. 13:1033
    [Google Scholar]
81. 81.  Schlünzen F, Zarivach R, Harms J, Bashan A, Tocilj A et al. 2001. Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. Nature 413:814–21
    [Google Scholar]
82. 82.  Schuwirth BS, Day JM, Hau CW, Janssen GR, Dahlberg AE et al. 2006. Structural analysis of kasugamycin inhibition of translation. Nat. Struct. Mol. Biol. 13:879–86
    [Google Scholar]
83. 83.  Seiple IB, Zhang Z, Jakubec P, Langlois-Mercier A, Wright PM et al. 2016. A platform for the discovery of new macrolide antibiotics. Nature 533:338–45
    [Google Scholar]
84. 84.  Shimizu Y, Inoue A, Tomari Y, Suzuki T, Yokogawa T et al. 2001. Cell-free translation reconstituted with purified components. Nat. Biotechnol. 19:751–55
    [Google Scholar]
85. 85.  Shinabarger DL, Marotti KR, Murray RW, Lin AH, Melchior EP et al. 1997. Mechanism of action of oxazolidinones: effects of linezolid and eperezolid on translation reactions. Antimicrob. Agents Chemother. 41:2132–36
    [Google Scholar]
86. 86.  Sievers A, Beringer M, Rodnina MV, Wolfenden R 2004. The ribosome as an entropy trap. PNAS 101:7897–901
    [Google Scholar]
87. 87.  Sothiselvam S, Liu B, Han W, Ramu H, Klepacki D et al. 2014. Macrolide antibiotics allosterically predispose the ribosome for translation arrest. PNAS 111:9804–9
    [Google Scholar]
88. 88.  Sothiselvam S, Neuner S, Rigger L, Klepacki D, Micura R et al. 2016. Binding of macrolide antibiotics leads to ribosomal selection against specific substrates based on their charge and size. Cell Rep 16:1–11
    [Google Scholar]
89. 89.  Starosta AL, Karpenko VV, Shishkina AV, Mikolajka A, Sumbatyan NV et al. 2010. Interplay between the ribosomal tunnel, nascent chain, and macrolides influences drug inhibition. Chem. Biol. 17:504–14
    [Google Scholar]
90. 90.  Subramanian SL, Ramu H, Mankin AS 2012. Inducible resistance to macrolide antibiotics. Antibiotic Drug Discovery and Development TJ Dougherty, MJ Pucci 455–484 New York: Springer
    [Google Scholar]
91. 91.  Tenson T, Lovmar M, Ehrenberg M 2003. The mechanism of action of macrolides, lincosamides and streptogramin B reveals the nascent peptide exit path in the ribosome. J. Mol. Biol. 330:1005–14
    [Google Scholar]
92. 92.  Tenson T, Mankin AS 2001. Short peptides conferring resistance to macrolide antibiotics. Peptides 22:1661–68
    [Google Scholar]
93. 93.  Tenson T, Xiong L, Kloss P, Mankin AS 1997. Erythromycin resistance peptides selected from random peptide libraries. J. Biol. Chem. 272:17425–30
    [Google Scholar]
94. 94.  Tu D, Blaha G, Moore PB, Steitz TA 2005. Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance. Cell 121:257–70
    [Google Scholar]
95. 95.  Udagawa T, Shimizu Y, Ueda T 2004. Evidence for the translation initiation of leaderless mRNAs by the intact 70 S ribosome without its dissociation into subunits in eubacteria. J. Biol. Chem. 279:8539–46
    [Google Scholar]
96. 96.  Vazquez D 1979. Inhibitors of Protein Biosynthesis Berlin: Springer-Verlag
97. 97.  Vázquez-Laslop N, Klepacki D, Mulhearn DC, Ramu H, Krasnykh O et al. 2011. Role of antibiotic ligand in nascent peptide-dependent ribosome stalling. PNAS 108:10496–501
    [Google Scholar]
98. 98.  Vázquez-Laslop N, Mankin AS 2014. Triggering peptide-dependent translation arrest by small molecules: ribosome stalling modulated by antibiotics. Regulatory Nascent Polypeptides K Ito 165–86 New York: Springer
    [Google Scholar]
99. 99.  Vázquez-Laslop N, Ramu H, Klepacki D, Kannan K, Mankin AS 2010. The key role of a conserved and modified rRNA residue in the ribosomal response to the nascent peptide. EMBO J 29:3108–17
    [Google Scholar]
100. 100.  Vázquez-Laslop N, Thum C, Mankin AS 2008. Molecular mechanism of drug-dependent ribosome stalling. Mol. Cell 30:190–202
     [Google Scholar]
101. 101.  Vesper O, Amitai S, Belitsky M, Byrgazov K, Kaberdina AC et al. 2011. Selective translation of leaderless mRNAs by specialized ribosomes generated by MazF in Escherichia coli. . Cell 147:147–57
     [Google Scholar]
102. 102.  Weisblum B 1995. Insights into erythromycin action from studies of its activity as inducer of resistance. Antimicrob. Agents Chemother. 39:797–805
     [Google Scholar]
103. 103.  Weissbach H, Redfield B, Brot N 1968. Studies on the reaction of N-acetyl-phenylalanyl-tRNA with puromycin. Arch. Biochem. Biophys. 127:705–10
     [Google Scholar]
104. 104.  Wilson DN 2009. The A-Z of bacterial translation inhibitors. Crit. Rev. Biochem. Mol. Biol. 44:393–433
     [Google Scholar]
105. 105.  Wilson DN, Schluenzen F, Harms JM, Starosta AL, Connell SR, Fucini P 2008. The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning. PNAS 105:13339–44
     [Google Scholar]
106. 106.  Wohlgemuth I, Brenner S, Beringer M, Rodnina MV 2008. Modulation of the rate of peptidyl transfer on the ribosome by the nature of substrates. J. Biol. Chem. 283:32229–35
     [Google Scholar]
107. 107.  Woodcock J, Moazed D, Cannon M, Davies J, Noller HF 1991. Interaction of antibiotics with A- and P-site-specific bases in 16S ribosomal RNA. EMBO J 10:3099–103
     [Google Scholar]
108. 108.  Youngman EM, Brunelle JL, Kochaniak AB, Green R 2004. The active site of the ribosome is composed of two layers of conserved nucleotides with distinct roles in peptide bond formation and peptide release. Cell 117:589–99
     [Google Scholar]