Bacterial transfer RNAs

FEMS Microbiology Reviews

Volumn 39, Issue 3, 2015, Pages 280-300

  Shepherd, Jennifer ^a   Ibba, Michael ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

Aminoacylation; Codon; Modification; Protein synthesis; Translation; tRNA

Indexed keywords

TRANSFER RNA; BACTERIAL RNA; CODON;

AMINOACYLATION; BACTERIAL CELL; BACTERIAL METABOLISM; CODON; NONHUMAN; PROTEIN MODIFICATION; REVIEW; RIBOSOME; RNA PROCESSING; RNA SYNTHESIS; GENE EXPRESSION REGULATION; GENETICS; METABOLISM;

CODON; GENE EXPRESSION REGULATION, BACTERIAL; RNA, BACTERIAL; RNA, TRANSFER;

EID: 84942062399     PISSN: 01686445     EISSN: 15746976     Source Type: Journal    
DOI: 10.1093/femsre/fuv004     Document Type: Review

References (311)

1. Abdi NM, Fredrick K. Contribution of 16S rRNA nucleotides forming the 30S subunit A and P sites to translation in Escherichia coli. RNA 2005;11:1624-32.
2. Agrawal A, Mohanty BK, Kushner SR. Processing of the seven valine tRNAs in Escherichia coli involves novel features of RNase P. Nucleic Acids Res 2014;42:1166-79.
3. Agris PF. Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications. EMBO Rep 2008;9:629-35.
4. Ahel I, Korencic D, Ibba M, et al. Trans-editing of mischarged tRNAs. P Natl Acad Sci USA 2003;100:15422-7.
5. Altman S. Isolation of tyrosine tRNA precursor molecules. Nat New Biol 1971;229:19-21.
6. Altman S. Biosynthesis of transfer RNA in Escherichia coli. Cell 1975;4:21-9.
7. Altman S Transfer RNA. Cambridge, MA: Massachusetts Institute of Technology, 1978.
8. Altman S, Kirsebom L. 14 Ribonuclease P. Cold Spring Harbor M 1999;37:351-80.
9. Altman S, Smith JD. Tyrosine tRNA precursor molecule polynucleotide sequence. Nat New Biol 1971;233:35-9.
10. Amberg R, Mizutani T, Wu XQ, et al. Selenocysteine synthesis in mammalia: an identity switch from tRNA(Ser) to tRNA(Sec). J Mol Biol 1996;263:8-19.
11. Amitsur M, Morad I, Kaufmann G. In vitro reconstitution of anticodon nuclease from components encoded by phage T4 and Escherichia coli CTr5X. EMBO J 1989;8:2411-5.
12. An S, Musier-Forsyth K. Cys-tRNA(Pro) editing by Haemophilus influenzae YbaK via a novel synthetase. YbaK. tRNA ternary complex. J Biol Chem 2005;280:34465-72.
13. Anderson P, Ivanov P. tRNA fragments in human health and disease. FEBS Lett 2014;588:4297-304.
14. Apirion D, Miczak A. RNA processing in prokaryotic cells. Bioessays 1993;15:113-20.
15. Asha PK, Blouin RT, Zaniewski R, et al. Ribonuclease BN: identification and partial characterization of a new tRNA processing enzyme. P Natl Acad Sci USA 1983;80:3301-4.
16. Asha PK, Deutscher MP. Escherichia coli CAN lacks a tRNAprocessing nuclease. J Bacteriol 1983;156:419-20.
17. Atherly AG, Menninger JR. Mutant E. coli strain with temperature sensitive peptidyl-transfer RNA hydrolase. Nat New Biol 1972;240:245-6.
18. Bailly M, Blaise M, Lorber B, et al. The transamidosome: a dynamic ribonucleoprotein particle dedicated to prokaryotic tRNA-dependent asparagine biosynthesis. Mol Cell 2007;28:228-39.
19. Baird NJ, Fang XW, Srividya N, et al. Folding of a universal ribozyme: the ribonuclease P RNA. Q Rev Biophys 2007;40: 113-61.
20. Baldwin AN, Berg P. Transfer ribonucleic acid-induced hydrolysis of valyladenylate bound to isoleucyl ribonucleic acid synthetase. J Biol Chem 1966;241:839-45.
21. Ban N, Nissen P, Hansen J, et al. The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 2000;289:905-20.
22. Banerjee R, Chen S, Dare K, et al. tRNAs: cellular barcodes for amino acids. FEBS Lett 2010;584:387-95.
23. Baron C, Bock A. The length of the aminoacyl-acceptor stem of the selenocysteine-specific tRNA(Sec) of Escherichia coli is the determinant for binding to elongation factors SELB or Tu. J Biol Chem 1991;266:20375-9.
24. Baron C, Westhof E, Bock A, et al. Solution structure of selenocysteine-inserting tRNA(Sec) from Escherichia coli. Comparison with canonical tRNA(Ser). J Mol Biol 1993;231:274-92.
25. Becker HD, Kern D. Thermus thermophilus: a link in evolution of the tRNA-dependent amino acid amidation pathways. P Natl Acad Sci USA 1998;95:12832-7.
26. Becker HD, Min B, Jacobi C, et al. The heterotrimeric Thermus thermophilus Asp-tRNA(Asn) amidotransferase can also generate Gln-tRNA(Gln). FEBS Lett 2000a;476:140-4.
27. Becker HD, Reinbolt J, Kreutzer R, et al. Existence of two distinct aspartyl-tRNA synthetases in Thermus thermophilus. Structural and biochemical properties of the two enzymes. Biochemistry 1997;36:8785-97.
28. Becker HD, Roy H, Moulinier L, et al. Thermus thermophilus contains an eubacterial and an archaebacterial aspartyl-tRNA synthetase. Biochemistry 2000b;39:3216-30.
29. Beebe JA, Fierke CA. A kinetic mechanism for cleavage of precursor tRNA(Asp) catalyzed by the RNA component of Bacillus subtilis ribonuclease P. Biochemistry 1994;33: 10294-304.
30. Beebe K, Ribas De Pouplana L, Schimmel P. Elucidation of tRNAdependent editing by a class II tRNA synthetase and significance for cell viability. EMBO J 2003;22:668-75.
31. Begley U, Dyavaiah M, Patil A, et al. Trm9-catalyzed tRNA modifications link translation to the DNA damage response. Mol Cell 2007;28:860-70.
32. Berk V, Zhang W, Pai RD, et al. Structural basis for mRNA and tRNA positioning on the ribosome. P Natl Acad Sci USA 2006;103:15830-4.
33. Bjork GR, Durand JM, Hagervall TG, et al. Transfer RNA modification: influence on translational frameshifting and metabolism. FEBS Lett 1999;452:47-51.
34. Bjork GR, Ericson JU, Gustafsson CE, et al. Transfer RNA modification. Annu Rev Biochem 1987;56:263-87.
35. Blanquet S, Mechulam Y, Schmitt E, Aminoacyl-transfer RNA maturation. In Lapointe J, Brakier-Gingras L (eds) Translation Mechanisms. New York: Kluwer Academic/Plenum Publishers 2003, 65-79.
36. Bock A, Hilgenfeld R, Tormay P, et al. Domain structure of the selenocysteine-specific translation factor SelB in prokaryotes. Biomed Environ Sci 1997;10:125-8.
37. Bonnefond L, Arai T, Sakaguchi Y, et al. Structural basis for nonribosomal peptide synthesis by an aminoacyltRNA synthetase paralog. P Natl Acad Sci USA 2011;108: 3912-7.
38. Bouhss A, Josseaume N, Severin A, et al. Synthesis of the Lalanyl- L-alanine cross-bridge of Enterococcus faecalis peptidoglycan. J Biol Chem 2002;277:45935-41.
39. Bugg TD. Bacterial peptidoglycan biosynthesis and its inhibition. In: Pinto BM (ed.) Comprehensive Natural Products Chemistry, Vol. 3. Elsevier: Amsterdam, 1999, 241-94.
40. Calendar R, Berg P. D-Tyrosyl RNA: formation, hydrolysis and utilization for protein synthesis. J Mol Biol 1967;26:39-54.
41. Carbon J, Squires C. Studies on genetically altered transfer RNA species in Escherichia coli. Cancer Res 1971;31:663-6.
42. Cassano AG, Anderson VE, Harris ME. Analysis of solvent nucleophile isotope effects: evidence for concerted mechanisms and nucleophilic activation by metal coordination in nonenzymatic and ribozyme-catalyzed phosphodiester hydrolysis. Biochemistry 2004;43:10547-59.
43. Chambers I, Frampton J, Goldfarb P, et al. The structure of the mouse glutathione peroxidase gene: the selenocysteine in the active site is encoded by the 'termination' codon, TGA. EMBO J 1986;5:1221-7.
44. Chan CT, Dyavaiah M, DeMott MS, et al. A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress. PLoS Genet 2010;6:e1001247.
45. Chen MW, Jahn D, Schon A, et al. Purification and characterization of Chlamydomonas reinhardtii chloroplast glutamyltRNA synthetase, a natural misacylating enzyme. J Biol Chem 1990;265:4054-7.
46. Chen RH, Buko AM, Whittern DN, et al. Pacidamycins, a novel series of antibiotics with anti-Pseudomonas aeruginosa activity. II. Isolation and structural elucidation. J Antibiot 1989;42: 512-20.
47. Cherayil JD, Bock RM. A column chromatographic procedure for the fractionation of s-RNA. Biochemistry 1965;4:1174-83.
48. Chong YE, Yang XL, Schimmel P. Natural homolog of tRNA synthetase editing domain rescues conditional lethality caused by mistranslation. J Biol Chem 2008;283:30073-8.
49. Cochella L, Brunelle JL, Green R. Mutational analysis reveals two independent molecular requirements during transfer RNA selection on the ribosome. Nat Struct Mol Biol 2007;14:30-6.
50. Commans S, Bock A. Selenocysteine inserting tRNAs: an overview. FEMS Microbiol Rev 1999;23:335-51.
51. Cone JE, Del Rio RM, Davis JN, et al. Chemical characterization of the selenoprotein component of clostridial glycine reductase: identification of selenocysteine as the organoselenium moiety. P Natl Acad Sci USA 1976;73:2659-63.
52. Crick FH. Codon-anticodon pairing: the wobble hypothesis. J Mol Biol 1966;19:548-55.
53. Cudny H, Deutscher MP. Apparent involvement of ribonuclease D in the 3' processing of tRNA precursors. P Natl Acad Sci USA 1980;77:37-841.
54. Curnow AW, Hong K, Yuan R, et al. Glu-tRNAGln amidotransferase: a novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. P Natl Acad Sci USA 1997;94:11819-26.
55. Curnow AW, Ibba M, Soll D. tRNA-dependent asparagine formation. Nature 1996;382:589-90.
56. Curnow AW, Tumbula DL, Pelaschier JT, et al. GlutamyltRNA(Gln) amidotransferase in Deinococcus radiodurans may be confined to asparagine biosynthesis. P Natl Acad Sci USA 1998;95:12838-43.
57. Cuzin F, Kretchmer N, Greenberg RE, et al. Enzymatic hydrolysis of N-substituted aminoacyl-tRNA. P Natl Acad Sci USA 1967;58:2079-86.
58. Dare K, Ibba M. Roles of tRNA in cell wall biosynthesis. Wiley Interdiscip Rev RNA 2012;3:247-64.
59. Dare K, Shepherd J, Roy H, et al. LysPGS formation in Listeria monocytogenes has broad roles in maintaining membrane integrity beyond antimicrobial peptide resistance. Virulence 2014;5:534-46.
60. Das G, Varshney U. Peptidyl-tRNA hydrolase and its critical role in protein biosynthesis. Microbiology 2006;152:2191-5.
61. Das M, Vargas-Rodriguez O, Goto Y, et al. Distinct tRNA recognition strategies used by a homologous family of editing domains prevent mistranslation. Nucleic Acids Res 2014;42: 3943-53.
62. Deutscher MP, Lin JJ, Evans JA. Transfer RNA metabolism in Escherichia coli cells deficient in tRNA nucleotidyltransferase. J Mol Biol 1977;117:1081-94.
63. Dickson LA, Schimmel PR. Structure of transfer RNAAMINOACYL TRANSFER RNA synthetase complexes investigated by nuclease digestion. Arch Biochem Biophys 1975;167:638-45.
64. Diner EJ, Beck CM, Webb JS, et al. Identification of a target cell permissive factor required for contact-dependent growth inhibition (CDI). Gene Dev 2012;26:515-25.
65. Dramsi S, Magnet S, Davison S, et al. Covalent attachment of proteins to peptidoglycan. FEMS Microbiol Rev 2008;32:307-20.
66. Dudock B, DiPeri C, Scileppi K, et al. The yeast phenylalanyltransfer RNA synthetase recognition site: the region adjacent to the dihydrouridine loop. P Natl Acad Sci USA 1971;68: 681-4.
67. Dunn JJ. RNase III cleavage of single-stranded RNA. Effect of ionic strength on the fideltiy of cleavage. J Biol Chem 1976;251: 3807-14.
68. Dunn JJ, Studier FW. T7 early RNAs and Escherichia coli ribosomal RNAs are cut from large precursor RNAs in vivo by ribonuclease 3. P Natl Acad Sci USA 1973;70:3296-300.
69. Dutka S, Meinnel T, Lazennec C, et al. Role of the 1-72 base pair in tRNAs for the activity of Escherichia coli peptidyl-tRNA hydrolase. Nucleic Acids Res 1993;21:4025-30.
70. Ebel JP, Giege R, Bonnet J, et al. Factors determining the specificity of the tRNA aminoacylation reaction. Non-absolute specificity of tRNA-aminoacyl-tRNA synthetase recognition and particular importance of the maximal velocity. Biochimie 1973;55:547-57.
71. Ehlert K, Tschierske M, Mori C, et al. Site-specific serine incorporation by Lif and Epr into positions 3 and 5 of the Staphylococcal peptidoglycan interpeptide bridge. J Bacteriol 2000;182:2635-8.
72. El Yacoubi B, BaillyM, de Crecy-Lagard V. Biosynthesis and function of posttranscriptional modifications of transfer RNAs. Annu Rev Genet 2012;46:69-95.
73. Eldred EW, Schimmel PR. Rapid deacylation by isoleucyl transfer ribonucleic acid synthetase of isoleucine-specific transfer ribonucleic acid aminoacylated with valine. J Biol Chem 1972;247:2961-4.
74. Emilsson V, Naslund AK, Kurland CG. Thiolation of transfer RNA in Escherichia coli varies with growth rate. Nucleic Acids Res 1992;20:4499-505.
75. Ericson JU, Bjork GR. Pleiotropic effects induced by modification deficiency next to the anticodon of tRNA from Salmonella typhimurium LT2. J Bacteriol 1986;166:1013-21.
76. Ernst CM, Peschel A. Broad-spectrum antimicrobial peptide resistance by MprF-mediated aminoacylation and flipping of phospholipids. Mol Microbiol 2011;80:290-9.
77. Ernst CM, Staubitz P, Mishra NN, et al. The bacterial defensin resistance proteinMprF consists of separable domains for lipid lysinylation and antimicrobial peptide repulsion. PLoS Pathog 2009;5:e1000660.
78. FarrowMA, Nordin BE, Schimmel P. Nucleotide determinants for tRNA-dependent amino acid discrimination by a class I tRNA synthetase. Biochemistry 1999;38:16898-903.
79. Ferri-Fioni ML, Schmitt E, Soutourina J, et al. Structure of crystalline D-Tyr-tRNA(Tyr) deacylase. A representative of a new class of tRNA-dependent hydrolases. J Biol Chem 2001;276:47285-90.
80. Filipe SR, Pinho MG, Tomasz A. Characterization of the murMN operon involved in the synthesis of branched peptidoglycan peptides in Streptococcus pneumoniae. J Biol Chem 2000;275:27768-74.
81. Filipe SR, Tomasz A. Inhibition of the expression of penicillin resistance in Streptococcus pneumoniae by inactivation of cell wall muropeptide branching genes. P Natl Acad Sci USA 2000;97:4891-6.
82. Findeiss S, Langenberger D, Stadler PF, et al. Traces of posttranscriptional RNA modifications in deep sequencing data. Biol Chem 2011;392:305-13.
83. Fiser A, Filipe SR, Tomasz A. Cell wall branches, penicillin resistance and the secrets of the MurM protein. Trends Microbiol 2003;11:547-53.
84. Fonvielle M, Chemama M, Villet R, et al. Aminoacyl-tRNA recognition by the FemXWv transferase for bacterial cell wall synthesis. Nucleic Acids Res 2009;37:1589-601.
85. Forchhammer K, Leinfelder W, Bock A. Identification of a novel translation factor necessary for the incorporation of selenocysteine into protein. Nature 1989;342:453-6.
86. Fournier MJ, Ozeki H. Structure and organization of the transfer ribonucleic acid genes of Escherichia coli K-12. Microbiol Rev 1985;49:379-97.
87. Friedman M. Chemistry, nutrition, and microbiology of D-amino acids. J Agr Food Chem 1999;47:3457-79.
88. Fromant M, Plateau P, Schmitt E, et al. Receptor site for the 5'- phosphate of elongator tRNAs governs substrate selection by peptidyl-tRNA hydrolase. Biochemistry 1999;38:4982-7.
89. Fukunaga R, Yokoyama S. Structure of the AlaX-M transediting enzyme from Pyrococcus horikoshii. Acta Crystallogr D 2007;63:390-400.
90. Gagnon Y, Lacoste L, Champagne N, et al. Widespread use of the glu-tRNAGln transamidation pathway among bacteria. A member of the alpha purple bacteria lacks glutaminyl-trna synthetase. J Biol Chem 1996;271:14856-63.
91. Garcia-Bustos JF, Chait BT, Tomasz A. Structure of the peptide network of pneumococcal peptidoglycan. J Biol Chem 1987;262:15400-5.
92. Garcia-Villegas MR, De La Vega FM, Galindo JM, et al. PeptidyltRNA hydrolase is involved in lambda inhibition of host protein synthesis. EMBO J 1991;10:3549-55.
93. Garg RP, Gonzalez JM, Parry RJ. Biochemical characterization of VlmL, a Seryl-tRNA synthetase encoded by the valanimycin biosynthetic gene cluster. J Biol Chem 2006;281:26785-91.
94. Garg RP, Ma Y, Hoyt JC, et al. Molecular characterization and analysis of the biosynthetic gene cluster for the azoxy antibiotic valanimycin. Mol Microbiol 2002;46:505-17.
95. Garg RP, Qian XL, Alemany LB, et al. Investigations of valanimycin biosynthesis: elucidation of the role of seryl-tRNA. P Natl Acad Sci USA 2008;105:6543-7.
96. Gegenheimer P, Apirion D. Processing of procaryotic ribonucleic acid. Microbiol Rev 1981;45:502-41.
97. Gehrig S, Eberle ME, Botschen F, et al. Identification of modifications in microbial, native tRNA that suppress immunostimulatory activity. J Exp Med 2012;209:225-33.
98. Ghora BK, Apirion D. Structural analysis and in vitro processing to p5 rRNA of a 9S RNA molecule isolated from an rnemutant of E. coli. Cell 1978;15:1055-66.
99. Ghosh RK, Deutscher MP. Purification of potential 3' processing nucleases using synthetic tRNA precursors. Nucleic Acids Res 1978;5:3831-42.
100. Giannouli S, Kyritsis A, Malissovas N, et al. On the role of an unusual tRNAGly isoacceptor in Staphylococcus aureus. Biochimie 2009;91:344-51.
101. Giege R, Sissler M, Florentz C. Universal rules and idiosyncratic features in tRNA identity. Nucleic Acids Res 1998;26:5017-35.
102. Gillam I, Millward S, Blew D, et al. The separation of soluble ribonucleic acids on benzoylated diethylaminoethylcellulose. Biochemistry 1967;6:3043-56.
103. Globisch D, Pearson D, Hienzsch A, et al. Systems-based analysis of modified tRNA bases. Angew Chem Int Edit 2011;50:9739-42.
104. Gondry M, Sauguet L, Belin P, et al. Cyclodipeptide synthases are a family of tRNA-dependent peptide bond-forming enzymes. Nat Chem Biol 2009;5:414-20.
105. Goodall JJ, Chen GJ, Page MG. Essential role of histidine 20 in the catalytic mechanism of Escherichia coli peptidyl-tRNA hydrolase. Biochemistry 2004;43:4583-91.
106. Grosjean H. DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution. Austin, TX: Landes Bioscience, 2009.
107. Grunberg-Manago M, Buckingham R, Cooperman B, et al. Structure and function of the translation Machinery. Symp Soc Gen Microbi 1978;28:27-110.
108. Gu C, Begley TJ, Dedon PC. tRNA modifications regulate translation during cellular stress. FEBS Lett 2014;588:4287-96.
109. Guenther UP, Yandek LE, Niland CN, et al. Hidden specificity in an apparently nonspecific RNA-binding protein. Nature 2013;502:385-8.
110. Guerrier-Takada C, Gardiner K, Marsh T, et al. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 1983;35:849-57.
111. Guillon JM, Heiss S, Soutourina J, et al. Interplay of methionine tRNAs with translation elongation factor Tu and translation initiation factor 2 in Escherichia coli. J Biol Chem 1996;271:22321-5.
112. Guillon JM, Mechulam Y, Blanquet S, et al. Importance of formylability and anticodon stem sequence to give a tRNA(Met) an initiator identity in Escherichia coli. J Bacteriol 1993;175: 4507-14.
113. Guillon JM, Mechulam Y, Schmitter JM, et al. Disruption of the gene for Met-tRNA(fMet) formyltransferase severely impairs growth of Escherichia coli. J Bacteriol 1992a;174:4294-301.
114. Guillon JM, Meinnel T, Mechulam Y, et al. Nucleotides of tRNA governing the specificity of Escherichia coli methionyltRNA(fMet) formyltransferase. J Mol Biol 1992b;224:359-67.
115. GuoM, Schimmel P. Structural analyses clarify the complex control of mistranslation by tRNA synthetases. Curr Opin Struct Biol 2012;22:119-26.
116. Gupta R. Halobacterium volcanii tRNAs. Identification of 41 tRNAs covering all amino acids, and the sequences of 33 class I tRNAs. J Biol Chem 1984;259:9461-71.
117. Gustilo EM, Vendeix FA, Agris PF. tRNA's modifications bring order to gene expression. Curr Opin Microbiol 2008;11:134-40.
118. Guth EC, Francklyn CS. Kinetic discrimination of tRNA identity by the conserved motif 2 loop of a class II aminoacyl-tRNA synthetase. Mol Cell 2007;25:531-42.
119. Guthrie C, Atchison R. Biochemical characterization of RNase P: a tRNA processing activity with protein and RNA components. Cold Spring Harbor M 1980;9:83-97.
120. Haas ES, Brown JW. Evolutionary variation in bacterial RNase P RNAs. Nucleic Acids Res 1998;26:4093-9.
121. Hale SP, Auld DS, Schmidt E, et al. Discrete determinants in transfer RNA for editing and aminoacylation. Science 1997;276:1250-2.
122. Harms J, Schluenzen F, Zarivach R, et al. High resolution structure of the large ribosomal subunit from a mesophilic eubacterium. Cell 2001;107:679-88.
123. Harris ME, Christian EL. Recent insights into the structure and function of the ribonucleoprotein enzyme ribonuclease P. Curr Opin Struct Biol 2003;13:325-33.
124. Hartmann E, Hartmann RK. The enigma of ribonuclease P evolution. Trends Genet 2003;19:561-9.
125. Haruna K, Alkazemi MH, Liu Y, et al. Engineering the elongation factor Tu for efficient selenoprotein synthesis. Nucleic Acids Res 2014;42:9976-83.
126. Hegde SS, Blanchard JS. Kinetic and mechanistic characterization of recombinant Lactobacillus viridescens FemX (UDP-Nacetylmuramoyl pentapeptide-lysine N6-alanyltransferase). J Biol Chem 2003;278:22861-7.
127. Hendrickson TL, Schimmel P. Transfer RNA-dependent amino acid discrimination by aminoacyl-tRNA synthetases. In Lapointe J, Brakier-Gingras L (eds) Translation Mechanisms. New York: Kluwer Academic/Plenum Publishers 2003; 34-64.
128. Heurgue-Hamard V, Karimi R, Mora L, et al. Ribosome release factor RF4 and termination factor RF3 are involved in dissociation of peptidyl-tRNA from the ribosome. EMBO J 1998;17:808-16.
129. Hilgenfeld R, Bock A, Wilting R. Structural model for the selenocysteine-specific elongation factor SelB. Biochimie 1996;78:971-8.
130. Hoagland MB, Keller EB, Zamecnik PC. Enzymatic carboxyl activation of amino acids. J Biol Chem 1956;218:345-58.
131. Hoagland MB, Stephenson ML, Scott JF, et al. A soluble ribonucleic acid intermediate in protein synthesis. J Biol Chem 1958;231:241-57.
132. Hoagland MB, Zamecnik PC, Stephenson ML. Intermediate reactions in protein biosynthesis. Biochim Biophys Acta 1957;24:215-6.
133. Holladay DW, Pearson RL, Kelmers AD. A general method for the separation of isoaccepting transfer ribonucleic acids: purification of five leucine transfer ribonucleic acids from Escherichia coli. Biochim Biophys Acta 1971;240:541-53.
134. Holley RW. Structure of an alanine transfer ribonucleic acid. JAMA 1965;194:868-71.
135. Holley RW, Apgar J, Everett GA, et al. Structure of a ribonucleic acid. Science 1965;147:1462-5.
136. Hong HJ, Hutchings MI, Hill LM, et al. The role of the novel Fem protein VanK in vancomycin resistance in Streptomyces coelicolor. J Biol Chem 2005;280:13055-61.
137. Hong HJ, Hutchings MI, Neu JM, et al. Characterization of an inducible vancomycin resistance system in Streptomyces coelicolor reveals a novel gene (vanK) required for drug resistance. Mol Microbiol 2004;52:1107-21.
138. Hopper AK, Phizicky EM. tRNA transfers to the limelight. Gene Dev 2003;17:162-80.
139. HooperML, Russell RL, Smith JD. Mischarging inmutant tyrosine transfer RNAs. FEBS Lett 1972;22:149-55.
140. Hou YM, Schimmel P. A simple structural feature is a major determinant of the identity of a transfer RNA. Nature 1988;333:140-5.
141. Hussain T, Kruparani SP, Pal B, et al. Post-transfer editing mechanism of a D-aminoacyl-tRNA deacylase-like domain in threonyl-tRNA synthetase from archaea. EMBO J 2006;25:4152-62.
142. Ibba M, Soll D. Aminoacyl-tRNA synthesis. Annu Rev Biochem 2000;69:617-50.
143. Ikemura T, Dahlberg JE. Small ribonucleic acids of Escherichia coli. I. Characterization by polyacrylamide gel electrophoresis and fingerprint analysis. J Biol Chem 1973a;248: 5024-32.
144. Ikemura T, Dahlberg JE. Small ribonucleic acids of Escherichia coli. II. Noncoordinate accumulation during stringent control. J Biol Chem 1973b;248:5033-41.
145. Jablonowski D, Schaffrath R. Zymocin, a composite chitinase and tRNase killer toxin from yeast. Biochem Soc T 2007;35:1533-7.
146. Jack RW, Jung G. Natural peptides with antimicrobial activity. CHIMIA 1998;52:48-55.
147. Johnson AE, Miller DL, Cantor CR. Functional covalent complex between elongation factor Tu and an analog of lysyl-tRNA. P Natl Acad Sci USA 1978;75:3075-9.
148. Jorgensen F, Kurland CG. Processivity errors of gene expression in Escherichia coli. J Mol Biol 1990;215:511-21.
149. Kaufmann G. Anticodon nucleases. Trends Biochem Sci 2000;25:70-4.
150. Kazantsev AV, Krivenko AA, Harrington DJ, et al. High-resolution structure of RNase P protein from Thermotoga maritima. P Natl Acad Sci USA 2003;100:7497-502.
151. Kazantsev AV, Krivenko AA, Harrington DJ, et al. Crystal structure of a bacterial ribonuclease P RNA. P Natl Acad Sci USA 2005;102:13392-7.
152. Kazantsev AV, Pace NR. Bacterial RNase P: a new view of an ancient enzyme. Nat Rev Microbiol 2006;4:729-40.
153. Keller W, Wolf J, Gerber A. Editing of messenger RNA precursors and of tRNAs by adenosine to inosine conversion. FEBS Lett 1999;452:71-6.
154. Khade P, Joseph S. Functional interactions by transfer RNAs in the ribosome. FEBS Lett 2010;584:420-6.
155. Kirsebom LA. RNase P RNA-mediated catalysis. Biochem Soc T 2002;30:1153-8.
156. Klein S, Lorenzo C, Hoffmann S, et al. Adaptation of Pseudomonas aeruginosa to various conditions includes tRNAdependent formation of alanyl-phosphatidylglycerol. MolMicrobiol 2009;71:551-65.
157. Konisky J. Colicins and other bacteriocins with established modes of action. Annu Rev Microbiol 1982;36:125-44.
158. Korostelev A, Trakhanov S, Laurberg M, et al. Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements. Cell 2006;126:1065-77.
159. Kossel H, RajBhandary UL. Studies on polynucleotides. LXXXVI. Enzymic hydrolysis of N-acylaminoacyl-transfer RNA. J Mol Biol 1968;35:539-60.
160. Krasilnikov AS, Xiao Y, Pan T, et al. Basis for structural diversity in homologous RNAs. Science 2004;306:104-7.
161. Krasilnikov AS, Yang X, Pan T, et al. Crystal structure of the specificity domain of ribonuclease P. Nature 2003;421:760-4.
162. Kromayer M, Wilting R, Tormay P, et al. Domain structure of the prokaryotic selenocysteine-specific elongation factor SelB. J Mol Biol 1996;262:413-20.
163. Kurland CG, Ehrenberg M. Constraints on the accuracy of messenger RNA movement. Q Rev Biophys 1985;18:423-50.
164. Lam SS, Schimmel PR. Equilibrium measurements of cognate and noncognate interactions between aminoacyl transfer RNA synthetases and transfer RNA. Biochemistry 1975;14:2775-80.
165. Lancaster L, Noller HF. Involvement of 16S rRNA nucleotides G1338 and A1339 in discrimination of initiator tRNA. Mol Cell 2005;20:623-32.
166. Lapointe J, Duplain L, Proulx M. A single glutamyl-tRNA synthetase aminoacylates tRNAGlu and tRNAGln in Bacillus subtilis and efficiently misacylates Escherichia coli tRNAGln1 in vitro. J Bacteriol 1986;165:88-93.
167. Lautru S, Gondry M, Genet R, et al. The albonoursin gene Cluster of S noursei biosynthesis of diketopiperazine metabolites independent of nonribosomal peptide synthetases. Chem Biol 2002;9:1355-64.
168. Lee BJ, de laPena P, Tobian JA, et al. Unique pathway of expression of an opal suppressor phosphoserine tRNA. P Natl Acad Sci USA 1987;84:6384-8.
169. Lee CP, Seong BL, RajBhandary UL. Structural and sequence elements important for recognition of Escherichia coli formylmethionine tRNA by methionyl-tRNA transformylase are clustered in the acceptor stem. J Biol Chem 1991;266:18012-7.
170. Lee JW, Beebe K, Nangle LA, et al. Editing-defective tRNA synthetase causes protein misfolding and neurodegeneration. Nature 2006;443:50-5.
171. Leinfelder W, Zehelein E, Mandrand-Berthelot MA, et al. Gene for a novel tRNA species that accepts L-serine and cotranslationally inserts selenocysteine. Nature 1988;331:723-5.
172. Leys D, Mowat CG, McLean KJ, et al. Atomic structure of Mycobacterium tuberculosis CYP121 to 1.06 A reveals novel features of cytochrome P450. J Biol Chem 2003;278:5141-7.
173. Li Z, Deutscher MP. Maturation pathways for E. coli tRNA precursors: a random multienzyme process in vivo. Cell 1996;86:503-12.
174. Li Z, Deutscher MP. RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors. RNA 2002;8:97-109.
175. Ling B, Berger-Bachi B. Increased overall antibiotic susceptibility in Staphylococcus aureus femAB null mutants. Antimicrob Agents Ch 1998;42:936-8.
176. Ling J, Reynolds N, Ibba M. Aminoacyl-tRNA synthesis and translational quality control. Annu Rev Microbiol 2009;63:61-78.
177. Lopes AP, Lopes LM, Fraga TR, et al. VapC from the leptospiral VapBC toxin-antitoxinmodule displays ribonuclease activity on the initiator tRNA. PLoS One 2014;9:e101678.
178. Lu J, Huang B, Esberg A, et al. The Kluyveromyces lactis gammatoxin targets tRNA anticodons. RNA 2005;11:1648-54.
179. Lund E, Dahlberg JE. Spacer transfer RNAs in ribosomal RNA transcripts of E. coli: processing of 30S ribosomal RNA in vitro. Cell 1977;11:247-62.
180. McDowall KJ, Lin-Chao S, Cohen SN. A+U content rather than a particular nucleotide order determines the specificity of RNase E cleavage. J Biol Chem 1994;269: 10790-6.
181. McFeeters RL. Recent antimicrobial developments targeting peptidyl-tRNA hydrolases. JSM Biotech Biomed Eng 2013;1:1006.
182. Maillard AP, Biarrotte-Sorin S, Villet R, et al. Structure-based sitedirected mutagenesis of the UDP-MurNAc-pentapeptidebinding cavity of the FemX alanyl transferase from Weissella viridescens. J Bacteriol 2005;187:3833-8.
183. Maloney E, Stankowska D, Zhang J, et al. The two-domain LysX protein of Mycobacterium tuberculosis is required for production of lysinylated phosphatidylglycerol and resistance to cationic antimicrobial peptides. PLoS Pathog 2009;5: e1000534.
184. Manley JL. Synthesis and degradation of termination and premature-termination fragments of beta-galactosidase in vitro and in vivo. J Mol Biol 1978;125:407-32.
185. Meineke B, Schwer B, Schaffrath R, et al. Determinants of eukaryal cell killing by the bacterial ribotoxin PrrC. Nucleic Acids Res 2011;39:687-700.
186. Menninger JR, Coleman RA. Lincosamide antibiotics stimulate dissociation of peptidyl-tRNA from ribosomes. Antimicrob Agents Ch 1993;37:2027-9.
187. Miczak A, Srivastava RA, Apirion D. Location of the RNAprocessing enzymes RNase III, RNase E and RNase P in the Escherichia coli cell. Mol Microbiol 1991;5:1801-10.
188. Miller D, Weissbach H. Factors involved in the transfer of aminoacyl-tRNA to the ribosome. In: Weissbach H, Moore S (eds). Molecular Mechanisms of Protein Biosynthesis. New York: Academic Press, 1977, 323-73.
189. Miller JP, Hussain Z, Schweizer MP. The involvement of the anticodon adjacent modified nucleoside N-(9-(BETA-Dribofuranosyl) purine-6-ylcarbamoyl)-threonine in the biological function of E. coli tRNAile. Nucleic Acids Res 1976;3:1185-201.
190. Moazed D, Noller HF. Intermediate states in the movement of transfer RNA in the ribosome. Nature 1989;342:142-8.
191. Mohanty BK, Kushner SR. Ribonuclease P processes polycistronic tRNA transcripts in Escherichia coli independent of ribonuclease E. Nucleic Acids Res 2007;35:7614-25.
192. Mohanty BK, Kushner SR. Rho-independent transcription terminators inhibit RNase P processing of the secG leuU and metT tRNA polycistronic transcripts in Escherichia coli. Nucleic Acids Res 2008;36:364-75.
193. Morl M, Marchfelder A. The final cut. The importance of tRNA 3'-processing. EMBO Rep 2001;2:17-20.
194. Motorin Y, Helm M. tRNA stabilization by modified nucleotides. Biochemistry 2010;49:4934-44.
195. Nakamura Y, Ito K. tRNA mimicry in translation termination and beyond. Wiley Interdiscip Rev RNA 2011;2:647-68.
196. Nameki N. Identity elements of tRNA(Thr) towards Saccharomyces cerevisiae threonyl-tRNA synthetase. Nucleic Acids Res 1995;23:2831-6.
197. Nawrot B, Sochacka E, Duchler M. tRNA structural and functional changes induced by oxidative stress. Cell Mol Life Sci 2011;68:4023-32.
198. Nicholson AW. Function, mechanism and regulation of bacterial ribonucleases. FEMS Microbiol Rev 1999;23:371-90.
199. Nikolaev N, Silengo L, Schlessinger D. A role for ribonuclease 3 in processing of ribosomal ribonucleic acid and messenger ribonucleic acid precursors in Escherichia coli. J Biol Chem 1973;248:7967-9.
200. Niranjanakumari S, Stams T, Crary SM, et al. Protein component of the ribozyme ribonuclease P alters substrate recognition by directly contacting precursor tRNA. P Natl Acad Sci USA 1998;95:15212-7.
201. Nissen P, Hansen J, Ban N, et al. The structural basis of ribosome activity in peptide bond synthesis. Science 2000;289: 920-30.
202. Noon KR, Guymon R, Crain PF, et al. Influence of temperature on tRNA modification in archaea: Methanococcoides burtonii (optimum growth temperature [Topt], 23 degrees C) and Stetteria hydrogenophila (Topt, 95 degrees C). J Bacteriol 2003;185:5483-90.
203. Novoa EM, Ribas de Pouplana L. Speeding with control: codon usage, tRNAs, and ribosomes. Trends Genet 2012;28:574-81.
204. Ogawa T, Tomita K, Ueda T, et al. A cytotoxic ribonuclease targeting specific transfer RNA anticodons. Science 1999;283: 2097-100.
205. Ogle JM, Brodersen DE, Clemons WM, et al. Recognition of cognate transfer RNA by the 30S ribosomal subunit. Science 2001;292:897-902.
206. Ogle JM, Carter AP, Ramakrishnan V. Insights into the decoding mechanism from recent ribosome structures. Trends Biochem Sci 2003;28:259-66.
207. Oku Y, Kurokawa K, Ichihashi N, et al. Characterization of the Staphylococcus aureus mprF gene, involved in lysinylation of phosphatidylglycerol. Microbiology 2004;150:45-51.
208. Ow MC, Kushner SR. Initiation of tRNA maturation by RNase E is essential for cell viability in E. coli. Gene Dev 2002;16: 1102-15.
209. Pace NR, Brown JW. Evolutionary perspective on the structure and function of ribonuclease P, a ribozyme. J Bacteriol 1995;177:1919-28.
210. Pan T. Adaptive translation as a mechanism of stress response and adaptation. Annu Rev Genet 2013;47:121-37.
211. Pang YL, Poruri K, Martinis SA. tRNA synthetase: tRNA aminoacylation and beyond. Wiley Interdiscip Rev RNA 2014;5:461-80.
212. Pape T, Wintermeyer W, Rodnina M. Induced fit in initial selection and proofreading of aminoacyl-tRNA on the ribosome. EMBO J 1999;18:3800-7.
213. Pearson RL, Weiss JF, Kelmers AD. Improved separation of transfer RNA's on polychlorotrifuoroethylene-supported reversed-phase chromatography columns. Biochim Biophys Acta 1971;228:770-4.
214. Penner M, Morad I, Snyder L, et al. Phage T4-coded Stp: doubleedged effector of coupled DNA and tRNA-restriction systems. J Mol Biol 1995;249:857-68.
215. Persson T, Cuzic S, Hartmann RK. Catalysis by RNase P RNA: unique features and unprecedented active site plasticity. J Biol Chem 2003;278:43394-401.
216. Petersen HU, Roll T, Grunberg-Manago M, et al. Specific interaction of initiation factor IF2 of E. coli with formylmethionyltRNA f Met. Biochem Bioph Res Co 1979;91:1068-74.
217. Peypoux F, Marion D, Maget-Dana R, et al. Structure of bacillomycin F, a new peptidolipid antibiotic of the iturin group. Eur J Biochem 1985;153:335-40.
218. Plautz G, Apirion D. Processing of RNA in Escherichia coli is limited in the absence of ribonuclease III, ribonuclease E and ribonuclease P. J Mol Biol 1981;149:813-9.
219. Pugsley AP. The ins and outs of colicins. Part I: production, and translocation across membranes. Microbiol Sci 1984a;1: 168-75.
220. Pugsley AP. The ins and outs of colicins. Part II. Lethal action, immunity and ecological implications. Microbiol Sci 1984b;1: 203-5.
221. Qin D, Abdi NM, Fredrick K. Characterization of 16S rRNA mutations that decrease the fidelity of translation initiation. RNA 2007;13:2348-55.
222. Raina M, Ibba M. tRNAs as regulators of biological processes. Front Genet 2014;5:171.
223. RajBhandary UL, Kohrer C. Early days of tRNA research: discovery, function, purification and sequence analysis. J Biosci 2006;31:439-51.
224. Randau L, Soll D. Transfer RNA genes in pieces. EMBO Rep 2008;9:623-8.
225. Ray BK, Apirion D. Transfer RNA precursors are accumulated in Escherichia coli in the absence of RNase E. Eur J Biochem 1981;114:517-24.
226. Reynolds NM, Lazazzera BA, Ibba M. Cellular mechanisms that control mistranslation. Nat Rev Microbiol 2010;8:849-56.
227. Robertson HD, Webster RE, Zinder ND. Purification and properties of ribonuclease III from Escherichia coli. J Biol Chem 1968;243:82-91.
228. Roe B, Sirover M, Dudock B. Kinetics of homologous and heterologous aminoacylation with yeast phenylalanyl transfer ribonucleic acid synthetase. Biochemistry 1973;12:4146-54.
229. Rohrer S, Berger-Bachi B. FemABX peptidyl transferases: a link between branched-chain cell wall peptide formation and beta-lactam resistance in gram-positive cocci. Antimicrob Agents Ch 2003;47:837-46.
230. Rohrer S, Ehlert K, Tschierske M, et al. The essential Staphylococcus aureus gene fmhB is involved in the first step of peptidoglycan pentaglycine interpeptide formation. P Natl Acad Sci USA 1999;96:9351-6.
231. Roy H, Ibba M. RNA-dependent lipid remodeling by bacterial multiple peptide resistance factors. P Natl Acad Sci USA 2008;105:4667-72.
232. Sakano H, Shimura Y. Sequential processing of precursor tRNA molecules in Escherichia coli. P Natl Acad Sci USA 1975;72: 3369-73.
233. Sakano H, Shimura Y. Characterization and in vitro processing of transfer RNA precursors accumulated in a temperaturesensitive mutant of Escherichia coli. J Mol Biol 1978;123: 287-326.
234. Schedl P, Roberts J, PrimakoffP. In vitro processing of E. coli tRNA precursors. Cell 1976;8:581-94.
235. Schimmel P. Mistranslation and its control by tRNA synthetases. Philos Tr R Soc Lon B 2011;366:2965-71.
236. Schimmel PR. Approaches to understanding the mechanism of specific protein-transfer RNA interactions. Accounts Chem Res 1977;10:411-8.
237. Schimmel PR, Uhlenbeck OC, Lewis JB, et al. Binding of complementary oligonucleotides to free and aminoacyl transfer ribonucleic acid synthetase bound transfer ribonucleic acid. Biochemistry 1972;11:642-6.
238. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972;36:407-77.
239. Schmeing TM, Huang KS, Strobel SA, et al. An induced-fit mechanism to promote peptide bond formation and exclude hydrolysis of peptidyl-tRNA. Nature 2005;438:520-4.
240. Schmidt FJ, McClain WH. An Escherichia coli ribonuclease which removes an extra nucleotide from a biosynthetic intermediate of bacteriophage T4 proline transfer RNA. Nucleic Acids Res 1978;5:4129-39.
241. Schmitt E, Blanquet S, Mechulam Y. Structure of crystalline Escherichia coli methionyl-tRNA(f)Met formyltransferase: comparison with glycinamide ribonucleotide formyltransferase. EMBO J 1996a;15:4749-58.
242. Schmitt E, Fromant M, Plateau P, et al. Crystallization and preliminary X-ray analysis of Escherichia coli peptidyl-tRNA hydrolase. Proteins 1997a;28:135-6.
243. Schmitt E, Mechulam Y, Fromant M, et al. Crystal structure at 1.2 A resolution and active site mapping of Escherichia coli peptidyl-tRNA hydrolase. EMBO J 1997b;16:4760-9.
244. Schmitt E, Mechulam Y, RuffM, et al. Crystallization and preliminary X-ray analysis of Escherichia coli methionyl-tRNA(fMet) formyltransferase. Proteins 1996b;25:139-41.
245. Schneider T, Senn MM, Berger-Bachi B, et al. In vitro assembly of a complete, pentaglycine interpeptide bridge containing cell wall precursor (lipid II-Gly5) of Staphylococcus aureus. Mol Microbiol 2004;53:675-85.
246. Schoemaker HJ, Schimmel PR. Photo-induced joining of a transfer RNAwith its cognate aminoacyl-transfer RNA synthetase. J Mol Biol 1974;84:503-13.
247. Schon A, Hottinger H, Soll D. Misaminoacylation and transamidation are required for protein biosynthesis in Lactobacillus bulgaricus. Biochimie 1988a;70:391-4.
248. Schon A, Kannangara CG, Gough S, et al. Protein biosynthesis in organelles requires misaminoacylation of tRNA. Nature 1988b;331:187-90.
249. Schulman LH, Pelka H. The structural basis for the resistance of Escherichia coli formylmethionyl transfer ribonucleic acid to cleavage by Escherichia coli peptidyl transfer ribonucleic acid hydrolase. J Biol Chem 1975;250:542-7.
250. Schulman LH, Pelka H. Structural requirements for aminoacylation of Escherichia coli formylmethionine transfer RNA. Biochemistry 1977;16:4256-65.
251. Seidman JG, Schmidt FJ, Foss K, et al. A mutant of escherichia coli defective in removing 3' terminal nucleotides from some transfer RNA precursor molecules. Cell 1975;5: 389-400.
252. Sekiya T, Contreras R, Takeya T, et al. Total synthesis of a tyrosine suppressor transfer RNA gene. XVII. Transcription, in vitro, of the synthetic gene and processing of the primary transcript to transfer RNA. J Biol Chem 1979;254:5802-16.
253. Selmer M, Dunham CM, Murphy FVt, et al. Structure of the 70S ribosome complexed with mRNA and tRNA. Science 2006;313:1935-42.
254. Seward HE, Roujeinikova A, McLean KJ, et al. Crystal structure of the Mycobacterium tuberculosis P450 CYP121-fluconazole complex reveals new azole drug-P450 binding mode. J Biol Chem 2006;281:39437-43.
255. Shepherd J. Characterisation of Pneumococcal Peptidoglycan Cross- Linking Enzymology. Thesis, University of Warwick, 2011.
256. Shepherd J, Ibba M. Direction of aminoacylated transfer RNAs into antibiotic synthesis and peptidoglycan-mediated antibiotic resistance. FEBS Lett 2013a;587:2895-904.
257. Shepherd J, Ibba M. Lipid II-independent trans editing of mischarged tRNAs by the penicillin resistance factorMurM. J Biol Chem 2013b;288:25915-23.
258. Shepherd J, Ibba M. Relaxed substrate specificity leads to extensive tRNA Mischarging by Streptococcus pneumoniae class I and Class II aminoacyl-tRNA synthetases. MBio 2014;5: e01656-14.
259. Shimura Y, Aono H, Ozeki H, et al. Mutant tyrosine tRNA of altered amino acid specificity. FEBS Lett 1972;22:144-8.
260. Shoji J, Hinoo H, Sakazaki R. The constituent amino acids and fatty acid of antibiotic 333-25. (Studies on antibiotics from the genus Bacillus. XII. J Antibiot (Tokyo) 1976;29:521-5.
261. Sivonen K, Namikoshi M, Evans WR, et al. Three new microcystins, cyclic heptapeptide hepatotoxins, from Nostoc sp. strain 152. Chem Res Toxicol 1992;5:464-9.
262. Smith D, Pace NR. Multiple magnesium ions in the ribonuclease P reaction mechanism. Biochemistry 1993;32:5273-81.
263. Smith JD, Celis JE. Mutant tyrosine transfer RNA that can be charged with glutamine. Nat New Biol 1973;243:66-71.
264. Smith JK, Hsieh J, Fierke CA. Importance of RNA-protein interactions in bacterial ribonuclease P structure and catalysis. Biopolymers 2007;87:329-38.
265. Soderbom F, Svard SG, Kirsebom LA. RNase E cleavage in the 5' leader of a tRNA precursor. J Mol Biol 2005;352:22-7.
266. Söll D, Abelson J Transfer RNA: Structure, Properties, and Recognition. New York: Cold Spring Harbor Laboratory 1979.
267. Söll D, RajBhandary UL. tRNA: Structure, Biosynthesis, and Function. Washington, DC: ASM Press 1995.
268. Soma A, Ikeuchi Y, Kanemasa S, et al. An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol Cell 2003;12:689-98.
269. Soutourina J, Blanquet S, Plateau P. D-tyrosyl-tRNA(Tyr) metabolism in Saccharomyces cerevisiae. J Biol Chem 2000a;275:11626-30.
270. Soutourina J, Plateau P, Blanquet S. Metabolism of D-aminoacyltRNAs in Escherichia coli and Saccharomyces cerevisiae cells. J Biol Chem 2000b;275:32535-42.
271. Soutourina J, Plateau P, Delort F, et al. Functional characterization of the D-Tyr-tRNATyr deacylase fromEscherichia coli. J Biol Chem 1999;274:19109-14.
272. Spitzfaden C, Nicholson N, Jones JJ, et al. The structure of ribonuclease P protein from Staphylococcus aureus reveals a unique binding site for single-stranded RNA. J Mol Biol 2000;295: 105-15.
273. Stams T, Niranjanakumari S, Fierke CA, et al. Ribonuclease P protein structure: evolutionary origins in the translational apparatus. Science 1998;280:752-5.
274. Stark BC, Kole R, Bowman EJ, et al. Ribonuclease P: an enzyme with an essential RNA component. P Natl Acad Sci USA 1978;75:3717-21.
275. Staubitz P, Neumann H, Schneider T, et al. MprF-mediated biosynthesis of lysylphosphatidylglycerol, an important determinant in staphylococcal defensin resistance. FEMS Microbiol Lett 2004;231:67-71.
276. Stern L, Schulman LH. The role of the minor base N4-acetylcytidine in the function of the Escherichia coli noninitiator methionine transfer RNA. J Biol Chem 1978;253:6132-9.
277. Stranden AM, Ehlert K, Labischinski H, et al. Cell wall monoglycine cross-bridges and methicillin hypersusceptibility in a femAB null mutant of methicillin-resistant Staphylococcus aureus. J Bacteriol 1997;179:9-16.
278. Strauch MA, Zalkin H, Aronson AI. Characterization of the glutamyl-tRNA(Gln)-to-glutaminyl-tRNA(Gln) amidotransferase reaction of Bacillus subtilis. J Bacteriol 1988;170: 916-20.
279. Sturchler C, Westhof E, Carbon P, et al. Unique secondary and tertiary structural features of the eucaryotic selenocysteine tRNA(Sec). Nucleic Acids Res 1993;21:1073-9.
280. Sugai M, Fujiwara T, Ohta K, et al. epr, which encodes glycylglycine endopeptidase resistance, is homologous to femAB and affects serine content of peptidoglycan cross bridges in Staphylococcus capitis and Staphylococcus aureus. J Bacteriol 1997;179:4311-8.
281. Sundari RM, Stringer EA, Schulman LH, et al. Interaction of bacterial initiation factor 2 with initiator tRNA. J Biol Chem 1976;251:3338-45.
282. Swairjo MA, Schimmel PR. Breaking sieve for steric exclusion of a noncognate amino acid from active site of a tRNA synthetase. P Natl Acad Sci USA 2005;102:988-93.
283. Thiebe R, Harbers K, Zachau HG. Aminoacylation of fragment combinations from yeast tRNA phe. Eur J Biochem 1972;26:144-52.
284. Toh Y, Hori H, Tomita K, et al. Transfer RNA synthesis and regulation. In: eLS. John Wiley & Sons Ltd, Chichester. 2001. http://www.els.net [doi:10.1002/9780470015902.a0000529.pub3]
285. Tomita K, Ogawa T, Uozumi T, et al. A cytotoxic ribonuclease which specifically cleaves four isoaccepting arginine tRNAs at their anticodon loops. P Natl Acad Sci USA 2000;97: 8278-83.
286. Torres-Larios A, Swinger KK, Krasilnikov AS, et al. Crystal structure of the RNA component of bacterial ribonuclease P. Nature 2005;437:584-7.
287. Torres-Larios A, Swinger KK, Pan T, et al. Structure of ribonuclease P-a universal ribozyme. Curr Opin Struct Biol 2006;16: 327-35.
288. Tschierske M, Ehlert K, Stranden AM, et al. Lif, the lysostaphin immunity factor, complements FemB in staphylococcal peptidoglycan interpeptide bridge formation. FEMS Microbiol Lett 1997;153:261-4.
289. Tschierske M, Mori C, Rohrer S, et al. Identification of three additional femAB-like open reading frames in Staphylococcus aureus. FEMS Microbiol Lett 1999;171:97-102.
290. Tumbula DL, Becker HD, Chang WZ, et al. Domain-specific recruitment of amide amino acids for protein synthesis. Nature 2000;407:106-10.
291. Uthman S, Kheir E, Bär C, Growth inhibition strategies based on antimicrobial microbes/toxins. In: Mendez-Vilas A (ed.). Science against Microbial Pathogens: Communicating Current Research and Technological Advances: Spain: Formatex Research Center, 2011, 1321-9.
292. Valle M, Zavialov A, Li W, et al. Incorporation of aminoacyl-tRNA into the ribosome as seen by cryo-electron microscopy. Nat Struct Biol 2003;10:899-906.
293. Voorhees RM, Weixlbaumer A, Loakes D, et al. Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nat Struct Mol Biol 2009;16:528-33.
294. Walker SC, Engelke DR. Ribonuclease P: the evolution of an ancient RNA enzyme. Crit Rev Biochem Mol 2006;41:77-102.
295. Waugh DS, Pace NR. Complementation of an RNase P RNA (rnpB) gene deletion in Escherichia coli by homologous genes from distantly related eubacteria. J Bacteriol 1990;172: 6316-22.
296. Weber B, Ehlert K, Diehl A, et al. The fib locus in Streptococcus pneumoniae is required for peptidoglycan crosslinking and PBP-mediated beta-lactam resistance. FEMS Microbiol Lett 2000;188:81-5.
297. Wegscheid B, Condon C, Hartmann RK. Type A and B RNase P RNAs are interchangeable in vivo despite substantial biophysical differences. EMBO Rep 2006;7:411-7.
298. Weissbach H. Molecular Mechanisms of Protein Biosynthesis. New York: Academic Press 1977.
299. Wetzel C, Limbach PA. Global identification of transfer RNAs by liquid chromatography-mass spectrometry (LC-MS). J Proteomics 2012;75:3450-64.
300. White BN, Bayley ST. Further codon assignments in an extremely halophilic bacterium using a cell-free proteinsynthesizing system and a ribosomal binding assay. Can J Biochem 1972;50:600-9.
301. Wilcox M. Gamma-glutamyl phosphate attached to glutaminespecific tRNA. A precursor of glutaminyl-tRNA in Bacillus subtilis. Eur J Biochem 1969;11:405-12.
302. Wilcox M, Nirenberg M. Transfer RNA as a cofactor coupling amino acid synthesis with that of protein. P Natl Acad Sci USA 1968;61:229-36.
303. Winther KS, Gerdes K. Enteric virulence associated protein VapC inhibits translation by cleavage of initiator tRNA. P Natl Acad Sci USA 2011;108:7403-7.
304. Wong FC, Beuning PJ, Silvers C, et al. An isolated class II aminoacyl-tRNA synthetase insertion domain is functional in amino acid editing. J Biol Chem 2003;278:52857-64.
305. Yamane T, Miller DL, Hopfield JJ. Discrimination between D- and L-tyrosyl transfer ribonucleic acids in peptide chain elongation. Biochemistry 1981;20:7059-64.
306. Yaniv M, Folk WR, Berg P, et al. A single mutational modification of a tryptophan-specific transfer RNA permits aminoacylation by glutamine and translation of the codon UAG. J Mol Biol 1974;86:245-60.
307. Yarus M, Berg P. Recognition of tRNA by aminoacyl tRNA synthetases. J Mol Biol 1967;28:479-90.
308. Yi C, Pan T. Cellular dynamics of RNA modification. Accounts Chem Res 2011;44:1380-8.
309. Zhang W, Ntai I, Bolla ML, et al. Nine enzymes are required for assembly of the pacidamycin group of peptidyl nucleoside antibiotics. J Am Chem Soc 2011a;133: 5240-3.
310. Zhang W, Ntai I, Kelleher NL, et al. tRNA-dependent peptide bond formation by the transferase PacB in biosynthesis of the pacidamycin group of pentapeptidyl nucleoside antibiotics. P Natl Acad Sci USA 2011b;108:12249-53.
311. Zinoni F, Birkmann A, Stadtman TC, et al. Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyaselinked) from Escherichia coli. P Natl Acad Sci USA 1986;83: 4650-4.