Chapter 47 : tRNA, tRNA Processing, and Aminoacyl-tRNA Synthetases

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Zoom in

tRNA, tRNA Processing, and Aminoacyl-tRNA Synthetases, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818388/9781555810535_Chap47-1.gif /docserver/preview/fulltext/10.1128/9781555818388/9781555810535_Chap47-2.gif


This chapter provides an overview of tRNA, tRNA processing, and tRNA synthetases in , emphasizing the areas in which there are distinct differences from . It discusses the general characteristics of tRNA in the gram-positive bacteria. Despite the common belief that most bacteria are similar to , the tRNA gene organization and anticodon complement in , and probably in most gram-positive bacteria, are remarkably different from those in i. The majority of the tRNA genes are in two large groups, one containing 21 and the other containing 16 tRNA genes, immediately following the 3′ ends of ribosomal gene operons. Ml-RNA has been shown to cleave modified tRNA-like substrates that consist of only the amino acid acceptor stem and the T-stem and loop. This explains how RNase P can recognize all of its tRNA precursor substrates and contrasts with the aminoacyl-tRNA synthetases that recognize many different nucleotide positions scattered throughout the tRNA. As aminoacyl-tRNA synthetases are so critical to the cell's metabolism, understanding their genetic regulation is especially important. Aminoacyl-tRNA synthetases have been divided into two classes on the basis of the presence of several different stretches of amino acid sequences. Class I synthetases include those for the amino acids arginine, glutamine, glutamate, isoleucine, leucine, methionine, tryptophan , tyrosine, and valine. Class II includes the aminoacyl-tRNA synthetases for aspartate, asparagine, histidine, lysine, phenylanine, proline, serine, and threonine.

Citation: Green C, Vold B. 1993. tRNA, tRNA Processing, and Aminoacyl-tRNA Synthetases, p 683-698. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch47
Highlighted Text: Show | Hide
Loading full text...

Full text loading...


Image of Figure 1
Figure 1

Known map positions of rRNA and tRNA operons on the chromosome divided into 360°. Numbers of genes in each tRNA gene cluster are indicated by arrows.

Citation: Green C, Vold B. 1993. tRNA, tRNA Processing, and Aminoacyl-tRNA Synthetases, p 683-698. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch47
Permissions and Reprints Request Permissions
Download as Powerpoint
Image of Figure 2
Figure 2

Gene orders of known tRNA gene clusters. Each tRNA gene is represented by a rectangle enclosing its cognate amino acid and anticodon. Map positions, where known, are listed above each operon. Putative promoters and terminators are labeled P and T, respectively.

Citation: Green C, Vold B. 1993. tRNA, tRNA Processing, and Aminoacyl-tRNA Synthetases, p 683-698. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch47
Permissions and Reprints Request Permissions
Download as Powerpoint


1. Adachi, T.,, H. Yamagata,, N. Tsukagoshi,, and S. Udaka. 1990. Use of both initiation sites of the middle wall protein gene in Bacillus brevis. J. Bacteriol. 172: 511 513.
2. Agris, P. F.,, H. Koh,, and D. Söll. 1973. The effect of growth temperature on the in vivo ribose methylation of Bacillus stearothermophilus transfer RNA. Arch. Biochem. Biophys. 154: 277 282.
3. Andachl, Y.,, F. Yamao,, A. Muto,, and S. Osawa. 1989. Codon recognition patterns as deduced from sequences of the complete set of transfer RNA species in Mycoplasma capricolum. J. Mol. Biol. 209: 37 54.
4. Armstrong, R. L.,, and N. Sueoka. 1968. Phase transitions in ribonucleic acid synthesis during germination of Bacillus subtilis spores. Proc. Natl. Acad. Set. USA 59: 153 160.
5. Arnold, H.,, and H. Kersten. 1973. The occurrence of ribothymidine, 1-methyladenosine, methylated gua-nosines and the corresponding methyltransferases in E. coli and Bacillus subtilis. FEBS Lett. 36: 34 38.
6. Arnold, H. J.,, W. Schmidt,, and H. Kersten. 1975. Occurrence and biosynthesis of ribothymidine in tRNA's of B. subtilis. FEBS Lett. 52: 62 65.
7. Bacot, C. M.,, and R. H. Reeves. 1991. Novel tRNA gene organization in the 16S-23S intergenic spacer of Streptococcus pneumoniae rRNA gene cluster. J. Bacteriol. 173: 4234 4236.
8. Balassa, G. 1966. Renouvellement des ARN et des protéines au cours de la sporulation de Bacillus subtilis. Ann. Inst. Pasteur 110: 316 346.
9. Barker, D. 1982. Cloning and amplified expression of the tyrosyl-tRNA synthetase genes of Bacillus stearothermophilus and Escherichia coll. Eur. J. Biochem. 125: 357 360.
10. Barstow, D. A.,, A. F. Sharman,, T. Atkinson,, and N. P. Minton. 1986. Cloning and complete nucleotide sequence of the Bacillus stearothermophilus tryptophanyl tRNA synthetase gene. Gene 46: 37 45.
11. Bhargava, S.,, A. K. Tyagi,, and J. S. Tyagi. 1990. tRNA genes in mycobacteria: organization and molecular cloning. J. Bacteriol. 172: 2930 2934.
12. Bhat, T. N.,, D. M. Blow,, and P. Brick. 1982. Tyrosyl-tRNA synthetase forms a mononucleotide-binding fold. J. Mol. Biol. 158: 699 709.
13. Björk, G. R.,, J. U. Ericson,, C. E. D. Gustafsson,, T. G. Hagervall,, Y. H. Jönsson,, and P. M. Wikström. 1987. Transfer RNA Modification. Annu. Rev. Biochem. 56: 263 287.
14. Bleyman, M.,, M. Kondo,, N. Hecht, and C. Woese. 1969. Transcriptional mapping: functional organization of the ribosomal and transfer ribonucleic acid cistrons in the Bacillus subtilis genome. J. Bacteriol. 99: 535 543.
15. Blow, D. M.,, T. N. Bhat,, A. Metcalfe,, J. L. Risler,, S. Brunie,, and C. Zelwer. 1983. Structural homology in the amino-terminal domains of two aminoacyl-tRNA synthetases. J. Mol. Biol. 171: 571 576.
16.Bonamy, C, L. Hirschbein, and J. Szulmajster. 1973. Synthesis of ribosomal ribonucleic acid during sporulation of Bacillus subtilis. J. Bacteriol. 113: 12961306.
17. Borgford, T. J.,, N. J. Brand,, T. E. Gray,, and A. R. Fersht. 1987. The valyl-tRNA synthetase from Bacillus stearothermophilus has considerable sequence homology with the isoleucyl-tRNA synthetase from Escherichia coli. Biochemistry 26: 2480 2486.
18. Bott, K. F.,, G. C. Stewart,, and A. G. Anderson,. 1984. Genetic mapping of cloned ribosomal RNA genes, p. 19 34. In A. T. Ganesan, and J. A. Hoch (ed.), Genetics and Biotechnology of the Bacilli. Academic Press, Inc., New York.
19. Brakhage, A. A.,, H. Putzer,, H. K. Shazand,, R. J. Röschenthaler,, and M. Grunberg-Manago. 1989. Bacillus subtilis phenylalanyl-tRNA synthetase genes: cloning and expression in Escherichia coli and B. subtilis. J. Bacteriol. 171: 1228 1232.
20. Brand, N. J.,, and A. R. Fersht. 1986. Molecular cloning of the gene encoding the valyl-tRNA synthetase from Bacillus stearothermophilus. Gene 44: 139 142.
21. Breton, R.,, D. Watson,, M. Yaguchi,, and J. Lapointe. 1990. Glutamyl-synthetases of Bacillus subtilis 168T and of Bacillus stearothermophilus: cloning and sequencing of the gltX genes and comparison with other aminoacyl-tRNA synthetases. J. Biol. Chem. 265: 18248 18255.
22. Brown, J. W.,, E. S. Haas,, B. D. James,, D. A. Hunt,, and N. R. Pace. 1991. Phylogenetic analysis and evolution of RNase P RNA in proteobacteria. J. Bacteriol. 173: 3855 3863.
23. Canard, B.,, and S. T. Cole. 1989. Genome organization of the anaerobic pathogen Clostridium perfringens. Proc. Natl. Acad. Sci. USA 86: 6676 6680.
24. Cerutti, P.,, J. W. Holt,, and N. Miller. 1968. Detection and determination of 5,6-dihydrouridine and 4-thiouri-dine in transfer ribonucleic acid from different sources. J. Mol. Biol. 34: 505 518.
25. Chen, M. W.,, D. Jahn,, A. Schön,, G. P. O'Neill,, and D. Soil. 1990. Purification and characterization of Chlamydomonas reinhardtii chloroplast glutamyl-tRNA synthetase, a naturally misacylating enzyme. J. Biol. Chem. 265: 4054 4057.
26. Chow, K.,, and J. T. Wong. 1988. Cloning and nucleotide sequence of the structural gene coding for Bacillus subtilis tryptophanyl-tRNA synthetase. Gene 73: 537 543.
27. Cooley, L.,, B. Appel,, and D. Soil. 1982. Post-transcrip-tional nucleotide addition is responsible for the formation of the 5' terminus of histidine. Proc. Natl. Acad. Sci. USA 79: 6475 6479.
28. Cortese, R. R.,, R. Landsberg,, R. A. Von der Haar,, H. E. Umbarger,, and B. N. Ames. 1974. Pleiotropy of hisT mutants blocked in pseudouridine synthesis in tRNA: leucine and isoleucine-valine operons. Proc. Natl. Acad. Sci. USA 71: 1857 1861.
29. Darr, S. C.,, K. Zito,, D. Smith,, and N. R. Pace. 1992. Contributions of phylogenetically variable structural elements to the function of the ribozyme ribonuclease P. Biochemistry 31: 328 333.
30. Delk, A. S.,, and J. C. Rabinowitz. 1975. Biosynthesis of ribosylthymine in the transfer RNA of Streptococcus faecalis: a folate-dependent methylation not involving S-adenosylmethionine. Proc. Natl. Acad. Sci. USA 72: 528 530.
31. Doi, R. H., 1969. Changes in nucleic acids during sporulation, p. 125 166. In G. W. Gould, and A. Hurst (ed.), The Bacterial Spore. Academic Press, London.
32. Duester, G. L.,, and W. M. Holmes. 1980. The distal end of the ribosomal RNA operon rmO of Escherichia coli contains a tRNAThrl gene, two 5S rRNA genes and a transcription terminator. Nucleic Acids Res. 8: 3793 3807.
33. Erlani, G.,, M. Delarue,, O. Poch,, J. Gangloff,, and D. Moras. 1990. Partition of tRNA synthetases into two classes based on mutually exclusive sets of sequence motifs. Nature (London) 347: 203 206.
34. Fayat, G.,, J. F. Mayaux,, C. Sacerdot,, M. Fromant,, M. Springer,, M. Grunberg-Manago,, and S. Blanquet. 1983. Escherichia coli phenyalanyl-tRNA synthetase operon region. Evidence for an attenuation mechanism. Identification of the gene for the ribosomal protein L20. J. Mol. Biol. 260: 10063 10068.
35. Fersht, A. R. 1987. Dissection of the structure and activity of the tyrosyl-tRNA synthetase by site-directed mutagenesis. Biochemistry 26: 8031 8037.
36. Forster, A. C.,, and R. H. Symons. 1987. Self-cleavage of plus and minus RNAs of a virusoid and a structural model for the active sites. Cell 49: 211 220.
37. Fournier, M. J.,, and H. Ozeki. 1985. Structure and organization of the tRNA genes of Escherichia coli K-12. Microbiol. Rev. 49: 379 397.
38. Fukada, K.,, and J. Abelson. 1980. DNA sequence of a T4 transfer RNA gene cluster. J. Mol. Biol. 139: 377 391.
39. Gardiner, K.,, and N. R. Pace. 1980. RNase P from Bacillus subtilis has an RNA component. J. Biol. Chem. 255: 7507 7509.
40. Giroux, S.,, J. Beaudet,, and R. Cedergren. 1988. Highly repetitive tRNAPr°-tRNAHis gene cluster from Photo-bacterium phosphoreum. J. Bacteriol. 170: 5601 5606.
41. Glaser, P.,, A. Danchin,, F. Kunst,, M. DéBarboullé,, A. Vertes,, and R. Dedonder. 1990. A gene encoding a tyrosine tRNA synthetase is located near sacS in Bacillus subtilis. Sequence-J. DNA Mapping Sequencing 1: 251 261.
42. Green, C. J.,, G. C. Stewart,, M. A. Hollis,, B. S. Vold,, and K. F. Bott. 1985. Nucleotide sequence of the Bacillus subtilis ribosomal RNA operon, rrriB. Gene 37: 261 266.
43. Green, C. J.,, and B. S. Void. 1983. Sequence analysis of a cluster of twenty-one tRNA genes in Bacillus subtilis. Nucleic Acids Res. 11: 5763 5774.
44. Green, C. J.,, and B. S. Void. 1988. Structural requirements for the processing of synthetic tRNAHis precursors by the catalytic RNA component of RNase P. J. Biol. Chem. 263: 652 657.
45. Green, C. J., and B. S. Void. 1992. A cluster of nine tRNA genes between ribosomal gene operons in Bacillus subtilis. J. Bacteriol. 174: 3147 3151.
46. Grunberg-Manago, M., 1987. Regulation of the expression of aminoacyl-tRNA synthetases and translation factors, p. 1386 1409. In F. C. Neidhardt,, J. L. Ingraham,, K. B. Low,, B. Magasanik,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. American Society for Microbiology, Washington, D.C.
47. Grundy, F. J.,, and T. M. Henkin. 1987. Cloning and analysis of the Bacillus subtilis rpsD gene, encoding ribosomal protein S4. J. Bacteriol. 172: 6372 6379.
48. Guerrier-Takada, C.,, K. Gardiner,, T. Marsh,, N. Pace,, and S. Altman. 1983. The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell 35: 849 857.
49. Gupta, R. 1984. Halobacterium volcanii tRNAs: identification of 41 tRNAs covering all amino acids, and the sequences of 33 class I tRNAs. J. Biol. Chem. 259: 9461 9471.
50. Haas, E. S.,, D. P. Morse,, J. W. Brown,, F. J. Schmidt,, and N. R. Pace. 1991. New long-range structure in ribonuclease P RNA. Science 254: 853 856.
51. Hager, P. W.,, and J. C. Rabinowitz,. 1985. Translational specificity in Bacillus subtilis, p. 1 32. In D. A. Dubnau (ed.), The Molecular Biology of the Bacilli, vol. 2. Academic Press, Inc., New York.
52. Hall, R. H. 1971. The Modified Nucleosides in Nucleic Acids. Columbia University Press, New York.
53. Hansen, F. G.,, E. B. Hansen,, and T. Atlung. 1985. Physical mapping and nucleotide sequence of the rnpA gene that encodes the protein component of ribonuclease P in Escherichia coli. Gene 38: 85 93.
54. Henkin, T. Personal communication.
55. Henner, D. J.,, and W. Steinberg. 1979. Transfer ribonu-cleic acid synthesis during sporulation and spore outgrowth in Bacillus subtilis studied by two-dimensional polyacrylamide gel electrophoresis. J. Bacteriol. 140: 555 566.
56. Hottinger, H.,, T. Ohgi,, M.-C. Zwahlen,, S. Dhamlja,, and D. Soil. 1987. Allele-specific complementation of an Escherichia coli leuB mutation by a Lactobacillus bul-garicus tRNA gene. Gene 60: 75 83.
57. Hsu, L. M.,, H. J. Klee,, J. Zagorskl,, and M. J. Fournter. 1984. Structure of an Escherichia coli tRNA operon containing linked genes for arginine, histidine, leucine, and proline tRNAs. J. Bacteriol. 158: 934 942.
58. Hussey, C.,, R. Losick,, and A. L. Sonenshein. 1971. Ribosomal RNA synthesis is turned off during sporulation of Bacillus subtilis. J. Mol. Biol. 57: 59 70.
59. Ikeda, R.,, T. Ohama,, A. Muto,, and S. Osawa. 1990. Nucleotide sequences of nine tRNA genes from Micrococcus luteus. Nucleic Acids Res. 18: 7154.
60. Ikeda, R.,, T. Ohama,, A. Muto,, and S. Osawa. 1990. Nucleotide sequences of two tRNA gene clusters from Micrococcus luteus. Nucleic Acids Res. 18: 7155.
61. Ikemura, T.,, and M. Nomura. 1977. Expression of spacer tRNA genes in ribosomal RNA transcription units by hybrid ColEl plasmids in E. coli. Cell 11: 779 793.
62. Jahn, D.,, Y.-C. Kim,, Y. Ishino,, M.-W. Chen,, and D. Soil. 1990. Purification and functional characterization of the Glu-tRNAGln amidotransferase from Chlamydomo-nas reinhardtii. J. Biol. Chem. 265: 8059 8064.
63. James, B. D.,, G. J. Olsen,, J. Liu,, and N. R. Pace. 1988. The secondary structure of a ribonuclease P RNA, the catalytic element of a ribonucleoprotein enzyme. Cell 52: 19 26.
64. Jarvis, E. D.,, R. L. Widom,, G. LaFauci,, Y. Setoguchi,, I. R. Richter,, and R. Rudner. 1988. Chromosomal organization of rRNA operons in Bacillus subtilis. Genetics 120: 625 635.
65. Jinks-Robertson, S.,, and M. Nomura,. 1987. Ribosomes and tRNA, p. 1358 1385. In F. C. Neidhardt,, J. L. Ingraham,, K. B. Low,, B. Magansanik,, M. Schaechter,, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. American Society for Microbiology, Washington, D.C.
66. Jones, M. D.,, D. M. Lowe,, T. Borgford,, and A. R. Fersht. 1986. Natural variations of tyrosyl-tRNA synthetase and comparison with engineered mutants. Biochemistry 25: 1887 1891.
67. Kashdan, M.,, and B. Dudock. 1982. The gene for a spinach chloroplast isoleucine tRNA has a methionine anticodon. J. Biol. Chem. 257: 11191 11194.
68. Keith, G.,, H. Rogg,, G. Dirheimer,, B. Menichi,, and T. Heyman. 1976. Post-transcriptional modification of tyrosine tRNA as a function of growth in Bacillus subtilis. FEBS Lett. 61: 120 122.
69. Kole, R.,, and S. Altman. 1979. Reconstitution of RNase P activity from inactive RNA and protein. Proc. Natl. Acad. Sci. USA 76: 3795 3799.
70. Komine, Y.,, T. Adachi,, H. Inokuchi,, and H. Ozeki. 1990. Genomic organization and physical mapping of the transfer RNA genes in Escherichia coli K12. J. Mol. Biol. 212: 579 598.
71. Komine, Y.,, and H. Inokuchi. 1991. Precise mapping of the mpB gene encoding the RNA component of RNase P in Escherichia coli K-12. J. Bacteriol. 173: 1813 1816.
72. Kozak, M. 1983. Comparison of initiation of protein synthesis in protein synthesis in procaryotes, eucaryotes, and organelles. Microbiol. Rev. 47: 1 45.
73. Kuchino, Y.,, S. Watanabe,, F. Harada,, and S. Nishimura. 1980. Primary structure of AUA specific isoleucine tRNA from Escherichia coli. Biochemistry 19: 2085 2089.
74. LaFauci, G.,, R. L. Widom,, R. L. Eisner,, E. D. Jarvis,, and R. Rudner. 1986. Mapping of rRNA genes with integrable plasmids in Bacillus subtilis. J. Bacteriol. 165: 204 214.
75. Lapointe, J.,, L. Duplan,, and M. Proulx. 1986. A single glutamyl-tRNA synthetase aminoacylates tRNAGlu and tRNA in Bacillus subtilis and efficiently misacylates Escherichia coli tRNAGlnl in vitro. J. Bacteriol. 165: 88 93.
76. Lee, J. S.,, G. An,, and J. D. Friesen. 1981. Location of the tufB promoter of E. coli: cotranscription of tufB with four transfer RNA genes. Cell 25: 251 258.
77. Losick, R.,, P. Youngman,, and P. J. Piggot. 1986. Genetics of endospore formation in Bacillus subtilis. Annu. Rev. Genet. 20: 625 669.
78. Loughney, K.,, E. Lund,, and J. E. Dahlberg. 1982. tRNA genes are found between the 16S and 23S rRNA genes in Bacillus subtilis. Nucleic Acids Res. 10: 1607 1624.
79. Lovett, P. S.,, N. P. Ambulos, Jr.,, W. Mulbry,, N. Noguchl,, and E. J. Rogers. 1991. UGA can be decoded as tryptophan at low efficiency in Bacillus subtilis. J. Bacteriol. 173: 1810 1812.
80. Lumelsky, N.,, and S. Altman. 1988. Selection and characterization of randomly produced mutants in the gene coding for Ml RNA. J. Mol. Biol. 202: 443 454.
81. Mandelstam, J., 1969. Regulation of bacterial spore formation, p. 377 401. In P. Meadow, and S. J. Pirt (ed.), Microbial Growth. Cambridge University Press, London.
82. Margulies, L.,, Y. Setoguchi,, and R. Rudner. 1978. Asymmetric transcription during post-germinative development of Bacillus subtilis spores. I. Hybridization patterns. Biochim. Biophys. Ada 521: 708 718.
83. Marsh, T. L.,, and N. R. Pace. 1985. Ribonuclease P catalysis differs from ribosomal RNA self-splicing. Science 229: 79 81.
84. Martin, N. C.,, M. Rabinowitz,, and H. Fukuhara. 1977. Yeast mitochondrial DNA specifies tRNA for 19 amino acids. Deletion mapping of the tRNA genes. Biochemistry 16: 4672 4677.
85. McClain, W. H.,, C. Guerrier-Takada,, and S. Altman. 1987. Model substrates for an RNA enzyme. Science 238: 527 530.
86. McLaughlin, J. R.,, C. L. Murray,, and J. C. Rabinowitz. 1981. Unique features in the ribosome binding sequence of the Gram-positive Staphylococcus aureus beta-lactamase gene. J. Biol. Chem. 256: 11283 11291.
87. Mechulam, Y.,, E. Schmitt,, M. Panvert,, J. Schmitter,, M. Lapadat-Tapolsky,, T. Meinnel,, P. Dessen,, S. Blanquet,, and G. Fayat. 1991. Methionyl-tRNA synthetase from Bacillus stearothermophilus: structural and functional identities with the Escherichia coli enzyme. Nucleic Acids Res. 19: 3673 3681.
88. Mézes, P. S. F.,, R. W. Blacher,, and J. O. Lampen. 1985. Processing of Bacillus cereus 569/H beta-lactamase I in Escherichia coli and Bacillus subtilis. J. Biol. Chem. 260: 1218 1223.
89. Miyajima, A.,, M. Shibuya,, Y. Kuchino,, and Y. Kaziro. 1981. Transcription of the E. coli tufB gene: cotran-scription with four tRNA genes and inhibition by guanosine-5'-diphosphate-3'-diphosphate. Mol. Gen. Genet. 189: 13 19.
90. Morgan, E. A.,, T. Ikemura,, L. Lindahl,, A. M. Fallon,, and M. Nomura. 1978. Some rRNA operons in E. coli have tRNA genes at their distal ends. Cell 13: 335 344.
91. Morgan, E. A.,, T. Ikemura,, and M. Nomura. 1977. Identification of spacer tRNA genes in individual ribosomal RNA transcription units of Escherichia coli. Proc. Natl. Acad. Sci. USA 74: 2710 2714.
92. Muto, A.,, Y. Andachi,, H. Yuzawa,, F. Yamao,, and S. Osawa. 1990. The organization and evolution of transfer RNA genes in Mycoplasma capricolum. Nucleic Acids Res. 18: 5037 5043.
93. Muto, A.,, T. Ohama,, Y. Andachi,, F. Yamao,, R. Tanaka,, and S. Osawa,. 1991. Evolution of codons and anti-codons in eubacteria, p. 179 193. In M. Kimura, and N. Takahata (ed.), New Aspects of the Genetics of Molecular Evolution. Japan Scientific Society Press, Tokyo.
94. Nakajlma, N.,, H. Ozekl,, and Y. Shimura. 1981. Organization and structure of an E. coli tRNA operon containing seven tRNA genes. Cell 23: 239 249.
95. Nieuwlandt, D. T.,, E. S. Haas, and C. J. Daniels. 1991. The RNA component of RNase P from the archaebac-terium Haloferax volcanii. J. Biol. Chem. 266: 5689 5695.
96. Ogasawara, N. 1985. Markedly unbiased codon usage in Bacillus subtilis. Gene 40: 145 150.
97. Ogasawara, N.,, S. Moriya,, K. von Meyenburg,, F. G. Hansen,, and H. Yoshikawa. 1985. Conservation of genes and their organization in the chromosomal replication origin region of Bacillus subtilis and Escherichia coli. EMBO J. 4: 3345 3350.
98. Ogasawara, N.,, S. Moriya,, and H. Yoshikawa. 1983. The structure and organization of rRNA operons at the region of the replication origin of the B. subtilis chromosome. Nucleic Acids Res. 11: 6301 6318.
99. Oishl, M.,, A. Oishi,, and N. Sueoka. 1966. Location of genetic loci of soluble RNA on Bacillus subtilis chromosome. J. Mol. Biol. 55: 1095 1103.
100. Orellana, O.,, L. Cooley,, and D. Soil. 1986. The additional guanylate at the 5'-end of Escherichia coli tRNAHIS is the result of unusual processing by RNase P. Mol. Cell. Biol. 6: 525 529.
101. Osawa, S.,, A. Muto,, T. H. Jukes,, and T. Ohama. 1990. Evolutionary changes in the genetic code. Proc. R. Soc. bond. Sect. B 241: 19 28.
102. Pace, N. R.,, C. Reich,, B. D. James,, G. J. Olsen,, B. Pace,, and D. S. Waugh. 1987. Structure and catalytic function in ribonuclease P. Cold Spring Harbor Symp. Quant. Biol. 52: 239 248.
103. Pace, N. R.,, D. K. Smith,, G. J. Olsen,, and B. D. James. 1989. Phylogenetic comparative analysis and the secondary structure of ribonuclease P RNA—a review. Gene 82: 65 75.
104. Pero, J.,, J. Nelson,, and R. Losick,. 1975. In vitro and in vivo transcription by vegetative and sporulating Bacillus subtilis, p. 202 212. In P. Gerhardt,, R. N. Costilow,, and H. L. Sadoff (ed.). Spores VI. American Society for Microbiology, Washington, D.C.
105. Piggot, P. J.,, M. Amjad,, J.-J. Wu,, H. Sandoval,, and J. Castro,. 1990. Genetic and physical maps of Bacillus subtilis 168, p. 493 534. In C. R. Harwood, and S. M. Cutting (ed.), Molecular Biology Methods for Bacillus. John Wiley & Sons Ltd., London.
106. Pittet, A. C.,, and H. Hottinger. 1989. Sequence of a hexameric tRNA gene cluster associated with rRNA genes in Lactobacillus bulgaricus. Nucleic Acids Res. 17: 4873.
107. Putney, S. D.,, and P. Schimmel. 1981. An aminoacyl tRNA synthetase binds to a specific DNA sequence and regulates its gene transcription. Nature (London) 291: 632 635.
108. Putzer, H.,, A. A. Brakhage,, and M. Grunberg-Manago. 1990. Independent genes for two threonyl-tRNA syn-thetases in Bacillus subtilis. J. Bacteriol. 172: 4593 4602.
109. Ramakrlshna, N.,, E. Dubnau,, and I. Smith. 1984. The complete DNA sequence and regulatory regions of the Bacillus licheniformis spoOH gene. Nucleic Acids Res. 12: 1779 1790.
110. Randerath, E.,, L.-L. S. Y. Chia,, H. P. Morris,, and K. Randerath. 1974. Base analysis of RNA by 3H postla-beling—a study of ribothymidine content and degree of base methylation of 4S RNA. Biochim. Biophys. Ada 366: 159 167.
111. Raue, H. A.,, and R. J. Planta. 1977. Heterogeneity of the genes coding for 5S RNA in three related strains of the genus Bacillus. Mol. Gen. Genet. 156: 185 193.
112. Reed, R. E.,, M. F. Baer,, C. Guerrier-Takada,, H. Donis-Kelier,, and S. Altman. 1982. Nucleotide sequence of the gene coding for the RNA subunit (Ml RNA) of ribonuclease P from Escherichia coli. Cell 30: 627 636.
113. Reich, C.,, K. J. Gardiner,, G. J. Olsen,, B. Pace,, T. L. Marsh,, and N. R. Pace. 1986. The RNA component of the Bacillus subtilis RNase P. J. Biol. Chem. 261: 7888 7893.
114. Reich, C.,, G. J. Olsen,, B. Pace,, and N. R. Pace. 1988. The role of the protein moiety of ribonuclease P, a ribonu-cleoprotein enzyme. Science 239: 178 181.
115. Rogers, M. J.,, J. Simmons,, R. T. Walker,, W. G. Weis-burg,, C. R. Woese,, R. S. Tanner,, I. M. Robinson,, D. A. Stahl,, G. Olsen,, R. H. Leach,, and J. Maniloff. 1985. Construction of the mycoplasma evolutionary tree from 5S rRNA sequence data. Proc. Natl. Acad. Sci. USA 82: 1160 1164.
116. Rogers, M. J.,, A. A. Steinmetz,, and R. T. Walker. 1987. Organization and structure of tRNA genes in Spiro-plasma melliferum. Isr. J. Med. Sci. 23: 357 360.
117. Rudner, R. Personal communication.
118. Samuelsson, T.,, P. Elias,, F. Lustig,, and Y. S. Guindy. 1985. Cloning and nucleotide sequence analysis of transfer RNA genes from Mycoplasma mycoides. Biochem. J. 232: 223 228.
119. Samuelsson, T.,, Y. S. Guindy,, F. Lustig,, T. Boren,, and U. Lagerkvist. 1987. Apparent lack of discrimination in the reading of certain codons in Mycoplasma mycoides. Proc. Natl. Acad. Sci. USA 84: 3166 3170.
120. Schimmel, P. 1987. Aminoacyl tRNA synthetases: general scheme of structure-function relationships in the polypeptides and recognition of transfer RNAs. Annu. Rev. Biochem. 56: 125 158.
121. Schmidt, F. J.,, and W. H. McClain. 1978. Alternate orders of processing by RNase P occur in vitro but not in vivo. J. Biol. Chem. 253: 4730 4734.
122. Schön, A.,, C. G. Kannangara,, S. Gough,, and D. Söll. 1988. Protein biosynthesis in organelles requires mis-aminoacylation of tRNA. Nature (London) 331: 187 190.
123. Schulman, L., 1979. Chemical approaches to the study of protein-tRNA recognition, p. 311 324. In P. R. Schimmel,, D. Soil,, and J. N. Abelson (ed.), Transfer RNA: Structure, Properties and Recognition. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
124. Setlow, P.,, G. Primuw,, and M. P. Deutscher. 1974. Absence of 3'-terminal residues from transfer ribonucleic acid of dormant spores of Bacillus megaterium. J. Bacteriol. 117: 127 132.
125. Setoguchi, Y.,, L. Margulies,, and R. Rudner. 1978. Asymmetric transcription during post-germinative development of Bacillus subtilis spores. II. Hybrid competition analyses. Biochim. Biophys. Acta 521: 719 725.
126. Singhal, R. P.,, and B. Void. 1976. Changes in transfer ribonucleic acids of Bacillus subtilu during different growth phases. Nucleic Acids Res. 3: 1249 1261.
127. Smith, D. W. E.,, A. L. McNamara,, and B. S. Void. 1982. Lysine tRNAs from Bacillus subtilis 168: function of the isoacceptors in a rabbit reticulocyte cell-free protein-synthesizing system. Nucleic Acids Res. 10: 3117 3123.
128. Smith, I.,, D. Dubnau,, P. Morell,, and J. Marmur. 1968. Chromosome location of DNA base sequences complementary to transfer RNA and to 5S, 16S and 23S ribosomal RNA in Bacillus subtilis. J. Mol. Biol. 33: 123 140.
129. Springer, M.,, M. Graffe,, J. S. Butler,, and M. Grunberg-Manago. 1986. Genetic definition of the translational operator of the threctnyl-tRNA synthetase gene in E. coli. Proc. Natl. Acad. Sci. USA 83: 4384 4388.
130. Sprinzl, M.,, N. Dank,, S. Nock,, and A. Schön. 1991. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 19( SuppI.): 2127 2171.
131. Sprinzl, M.,, T. Hartman,, J. Weber,, J. Blank,, and R. Zeidler. 1989. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res. 17: rl- rl72.
132. Stark, B. C.,, R. Kole,, E. J. Bowman,, and S. Altman. 1978. Ribonuclease P: an enzyme with an essential RNA component Proc. Natl. Acad Sci. USA 75: 3717 3721.
133. Strauch, M. A.,, H. Zalkin,, and A. I. Aronson. 1988. Characterization of the glutamyl-tRNAGln-to-glutaminyl-tRNAGln amidotransferase reaction of Bacillus subtilis. J. Bacteriol. 170: 916 920.
134. Testa, D.,, and R. Rudner. 1975. Synthesis of ribosomal RNA during sporulation in Bacillus subtilis. Nature ( London) 254: 630 632.
135. Thurlow, D. L.,, D. Shilowski,, and T. L. Marsh. 1991. Nucleotides in precursor tRNAs that are required intact for catalysis by RNase P RNAs. Nucleic Acids Res. 19: 885 891.
136. Void, B. 1974. Degree of completion of 3'-terminus of transfer ribonucleic acids of Bacillus subtilis 168 at various developmental stages and asporogenous mutants. J. Bacteriol. 117: 1361 1362.
137. Void, B. 1976. Modified nucleosides of Bacillus subtilis transfer ribonucleic acids. J. Bacteriol. 127: 258 267.
138. Void, B. S. 1973. Variations in activity of aminoacyl-tRNA synthetases as a function of development in Bacillus subtilis. Arch. Biochem. Biophys. 154: 691 695.
139. Void, B. S. 1973. Analysis of isoaccepting transfer ribonucleic acid species of Bacillus subtilis: chromato-graphic differences between transfer ribonucleic acids from spores and cells in exponential growth. J. Bacteriol. 113: 825 833.
140. Void, B. S. 1978. Post-transcriptional modifications of the anticodon loop region: alterations in isoaccepting species of tRNA's during development in Bacillus subtilis. J. Bacteriol. 135: 124 132.
141. Void, B. S. 1985. Structure and organization of genes for transfer ribonucleic acid in Bacillus subtilis. Microbiol. Rev. 49: 71 80.
142. Vold, B. S.,, and C. J. Green. 1986. Expression in Escherichia coli of Bacillus subtilis tRNA genes from a promoter within the tRNA gene region. J. Bacteriol. 166: 306 312.
143. Void, B. S.,, C. J. Green,, N. Narasimhan,, M. Strem,, and J. N. Hansen. 1988. Transcriptional analysis of Bacillus subtilis rRNA-tRNA operons. Unique properties of an operon containing a minor 5S rRNA gene. J. Biol. Chem. 263: 14485 14490.
144. Void, B. S.,, M. E. Longmire,, and D. E. Keith, Jr. 1981. Thiolation and 2-methylthio-modification of Bacillus subtilis transfer ribonucleic acids. J. Bacteriol. 148: 869 876.
145. Void, B. S.,, and S. Mlnatogawa,. 1972. Characterization of changes in transfer ribonucleic acids during sporulation in Bacillus subtilis, p. 254 263. In H. O. Halvorson,, R. Hanson,, and L. L. Campbell (ed.), Spores V. American Society for Microbiology, Washington, D.C.
146. Void, B. S.,, K. O. Okamoto,, B. J. Murphy,, and C. J. Green. 1988. Transcriptional analysis of Bacillus subtilis rRNA-tRNA operons. The tRNA gene cluster of rmB has an internal promoter. J. Biol. Chem. 263: 14480 14484.
147. Waugh, D. S.,, C. J. Green,, and N. R. Pace. 1989. The design and catalytic properties of a simplified ribonuclease P RNA. Science 244: 1569 1571.
148. Waugh, D. S.,, and N. R. Pace. 1990. Complementation of an RNase P RNA (rnpB) gene deletion in Escherichia coli by homologous genes from distantly related eubac-teria. J. Bacteriol. 172: 6316 6322.
149. Wawrousek, E. F.,, and J. N. Hansen. 1983. Structure and organization of a cluster of six tRNA genes in the space between tandem ribosomal RNA gene sets in Bacillus subtilis. J. Biol. Chem. 258: 291 299.
150. Wawrousek, E. F.,, N. Narasimhan,, and J. N. Hansen. 1984. Two large clusters with thirty-seven transfer RNA genes adjacent to ribosomal RNA gene sets in Bacillus subtilis: sequence and organization of trrnD and trrnE clusters. J. Biol. Chem. 259: 3694 3702.
151. Weisburg, W. G.,, J. G. Tully,, D. L. Rose,, J. P. Petzel,, H. Oyaizu,, D. Yang,, L. Mandeloo,, J. Sechrest,, T. G. Lawrence,, J. van Etten,, J. Maniloff, and C. R. Woese. 1989. A phyloge-netic analysis of the mycoplasmas: basis for their classification. J. Bacteriol. 171: 6455 6467.
152. White, B. N.,, and S. T. Bayley. 1972. Further codon assignments in an extremely halophilic bacterium using a cell-free protein-synthesizing system and a ribosomal binding assay. Can. J. Biochem. 50: 601 609.
153. Widom, R. L.,, E. D. Jarvis,, G. LaFauci,, and R. Rudner. 1988. Instability of rRNA operons in Bacillus subtilis. J. Bacteriol. 170: 605 610.
154. Wilcox, M. 1969. rPhosphoryl ester of Glu-tRNAGln as an intermediate in Bacillus subtilis glutaminyl-tRNA synthesis. Cold Spring Harbor Symp. Quant. Biol. 34: 521 528.
155. Wilcox, M. 1969. γ-Glutamyl phosphate attached to glutamine-specific tRNA. Eur. J. Biochem. 11: 405 412.
156. Wilcox, M.,, and M. Nirenberg. 1968. Transfer RNA as a cofactor coupling amino acid synthesis with that of protein. Proc. Natl. Acad. Sci. USA 61: 229 236.
157. Winter, G.,, G. L. E. Koch,, B. S. Hartley,, and D. G. Barker. 1983. The amino acid sequence of the tyrosyl-tRNA synthetase from Bacillus stearothermophilus. Eur. J. Biochem. 132: 383 387.
158. Yamada, Y.,, and H. Ishikura. 1980. Nucleotide sequence of non-initiator methionine tRNA from Bacillus subtilis. Nucleic Acids Res. 8: 4517 4520.
159. Yamada, Y.,, Y. Kuchino,, and H. Ishikura. 1980. Nucleotide sequence of initiator tRNA from Bacillus subtilis. J. Biochem. 87: 1261 1269.
160. Yamada, Y.,, M. Ohki,, and H. Ishikura. 1983. The nucleotide sequence of Bacillus subtilis tRNA genes. Nucleic Acids Res. 11: 3037 3045.
161. Yamagata, H.,, T. Adachi,, A. Tsuboi,, M. Takao,, T. Sasaki,, N. Tsukagoshi,, and S. Udaka. 1987. Cloning and characterization of the 5' region of the cell wall protein gene operon in Bacillus brevis 47. J. Bacteriol. 169: 1239 1245.
162. Yamao, F.,, A. Muto,, Y. Kawauchi,, M. Iwaml,, S. Iwag-ami,, Y. Azumi,, and S. Osawa. 1985. UGA is read as tryptophan in Mycoplasma capricolum. Proc. Natl. Acad. Sci. USA 82: 2306 2309.
163. Zaug, A. J.,, P. J. Grabowski,, and T. R. Cech. 1983. Autocatalytic cyclization reaction of an excised intervening sequence RNA is a cleavage-ligation reaction. Nature (London) 301: 578 583.
164. Zuber, P. A. 1982. Ph.D. thesis. University of Virginia, Charlottesville.


Generic image for table
Table 1

tRNA anticodons compared with and anticodons

Citation: Green C, Vold B. 1993. tRNA, tRNA Processing, and Aminoacyl-tRNA Synthetases, p 683-698. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch47

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error