Chapter 11 : Biosynthesis and Function of Modified Nucleosides

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Modified nucleosides, which are derivatives of the four normal nucleosides, adenosine (A), guanosine (G), cytidine (C), and uridine (U), were found in nucleic acids as early as 1948. Modified nucleosides are contained in tRNA from all three phylogenetic domains—Archaea, Bacteria, and Eucarya—which were formerly called the kingdoms of archaebacteria, eubacteria, and eukaryotes, respectively. Although modified nucleosides are found in various positions in the tRNA, two positions, 34 and 37, contain the largest variety of modified nucleosides. This chapter presents an overview of the coding properties associated with modified nucleosides present in positions 34 and 37. Outside the anticodon, the modified nucleosides are usually “simple” modifications like methylated or thiolated derivatives, whereas all except one (archaeosine in tRNAs from Archaea) of the hypermodified nucleosides are present in the anticodon region and only in positions 34 and 37. Moreover, outside the anticodon region, only one or two kinds of modified nucleosides in each position are present, whereas a large variety of modified nucleosides are present in the anticodon region, especially in positions 34 and 37. During evolution, structural refinements of the individual tRNAs were presumably fulfilled by the evolution of the synthesis of the various modified nucleosides, including the hypermodified nucleoside. Modified nucleosides in the anticodon region exert their functions primarily in the decoding process, whereas modified nucleosides outside this region may primarily be involved in other tRNA interactions, such as interactions with translation factors or as sensors for environmental stress conditions.

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11

Key Concept Ranking

Gene Expression and Regulation
Bacteria and Archaea
DNA Synthesis
Aromatic Amino Acids
Brome mosaic virus
Amino Acid Addition
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Image of Figure 1
Figure 1

Genetic organization of region (from reference with permission). FIS = possible FIS binding site; tRNA T-arm homology = a sequence with extensive similarity to the T-loop of tRNAs; AdoMet binding = AdoMet binding site; and catalytic nucleophile = the catalytic nucleophile Cys-324. Also shown are the similarity between the P and the P1 promoter of genes and the transcriptional terminator (T) shared with the gene. The gene is the structural gene for the vitamin B receptor. The sequence is found in reference .

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Image of Figure 2
Figure 2

Genetic organization of operon. Figures above the gene symbols indicate the number of protein molecules encoded from the respective genes per genome equivalents in cells grown at k = 1.0 hr. The Ω denotes a -independent terminator. In vitro, 60% to 70% of the transcript terminates at the first such structure ( ). Structures above the operon denote possible stem-loop structures that influence the translation of the and genes, respectively ( ). The sequence is found in reference .

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Image of Figure 3
Figure 3

Genetic organization of operon. Figures within the parentheses indicate the size of the protein encoded by the respective genes. Dyad symmetries and possible independent terminators are denoted as → ← and Ω, respectively. Transcriptions are shown by wavy lines and the transcription pattern is only tentative, since none of the transcripts has been shown to exist in vivo. The pattern is deduced from S1 mapping of a few areas of the operon, primer extension analysis, and analysis of polarity ( ). It is presently unclear whether and are part of the operon ( ). However, a chromosomally encoded transcript covering the intracistronic region between and is present ( ). Furthermore, the -independent terminator present between and is not active ( ), suggesting that transcripts extend to the -independent terminator following the gene. The promoters P, P, and P were located on the chromosome ( ), whereas P was located on a plasmid ( ). The dedD gene seems to have its own promoter located within the gene ( ). The overlap of the asd stop codon with the start codon is also indicated, suggesting translational coupling of the expression of these two genes ( ). The sequence is found in references and .

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Image of Figure 4
Figure 4

Genetic organization of operon. The sequence is found in reference . The location of the different promoters was established by H.-C. T. Tsui and M. Winkler ( ). Also shown is the region of translational overlap between the and genes and that translation terminates with UGA for both genes.

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Image of Figure 5
Figure 5

Genetic organization of the operon ( ). The sequence is found in reference .

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Image of Figure 6
Figure 6

Structure of queuosine and its derivatives.

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Image of Figure 7
Figure 7

Presence of modified nucleosides in position 34 (wobble position). Data compiled from reference . To the left of the different modified nucleosides are bars indicating which codons the tRNA is able to read well (filled circles). An open circle denotes less preferred pairing to that codon. Underlined nucleosides are for tRNAs from . If not otherwise stated N is an uncharacterized modified nucleoside and U* indicates a modified U; V4 = cmnmU; V5 = cmnms2U; V8 = mcnmU; V9 =cmnmUm.

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Figure 8

Synthesis of msioA37 and mcmoU and the links to the synthesis of chorismic acid.

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Image of Figure 9
Figure 9

Presence of modified nucleosides in position 37 (next to the 3-side of the anticodon) and the coding capacities of tRNAs. Note also that contains msioA instead of msiA in corresponding tRNAs (see Fig. 8 ) ( ). For explanation of symbols, see Fig. 1. Y1 (yW) = wybutosine; Y2 (oyW) = wybutoxosine; A4 = iA; A5 = msiA; Z = cis-zeatin or ioA; N for AAG codon is a modified A, probably a tA derivative.

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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Figure 10

Enzymatic mechanism for the synthesis of mU54. The figure is modified from reference .

Citation: Björk G. 1995. Biosynthesis and Function of Modified Nucleosides, p 165-205. In tRNA. ASM Press, Washington, DC. doi: 10.1128/9781555818333.ch11
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1. Abrell, J. W.,, E. E. Kaufman,, and M. N. Lipsett. 1971. The biosynthesis of 4-thiouridylate. Separation and purification of two enzymes in the transfer ribonucleic acid-sul-fertransferase system. J. Biol. Chem. 246:294301.
2. Achsel, T.,, and H. J. Gross. 1993. Identity determinants of human tRNASer: sequence elements necessary for serylation and maturation of tRNA with a long extra arm. EMBO J. 12:33333338.
3. Agris, P. F.,, D. J. Armstrong,, K. P. Schafer,, and D. Soli. 1975. Maturation of a hypermodified nucleoside in transfer RNA. Nucleic Acids Res. 2:691698.
4. Agris, P. F.,, H. Koh,, and D. Soli. 1973. The effect of growth temperatures on the in vivo ribose methylation of Bacillus stearothermophilus transfer RNA. Arch. Biochem. Biophys. 154:277282.
5. Agris, P. F.,, T. Play,, L. Goldman,, E. Horton,, D. Woolverton,, D. Setzer,, and C. Rodi. 1983. Processing of tRNA is accomplished by a high molecular-weight enzyme complex. Recent Results Cancer Res. 84:237254.
6. Agris, P. F.,, H. Sierzputowska-Gracz,, W. Smith,, A. Malkiewicz,, E. Sochacka,, and B. Nawrot. 1992. Thiolation of uridine carbon-2 restricts the motional dynamics of the transfer RNA wobble position nucleoside. J. Am. Chem. Soc. 114:26522656.
7. Agris, P. F.,, D. Söll,, and T. Seno. 1973. Biological function of 2-thiouridine in Escherichia coli glutamic acid transfer ribonucleic acid. Biochemistry 12:43314337.
8. Agris, P. F.,, D. K. Woolverton,, and D. Setzer. 1976. Subcellular localization of S-adenosyl-L-methionine:tRNA methyltransferases with aminoacyl-tRNA synthetases in human and mouse: normal and leukemic leukocytes. Proc. Natl. Acad. Sci. USA 73:38573861.
9. Andachi, Y.,, F. Yamao,, M. Iwami,, A. Muto,, and S. Osawa. 1987. Occurrence of unmodified adenine and uracil at the first position of anticodon in threonine tRNAs in Mycoplasma capricolum. Proc. Natl. Acad. Sci. USA 84:73987404.
10. Andachi, 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. Resemblance to mitochondria. J. Mol. Biol. 209:3754.
11. Arena, F.,, G. Ciliberto,, S. Ciampi,, and R. Cortese. 1978. Purification of pseudouridylate synthetase I from Salmonella typhimurium. Nucleic Acids Res. 5:45234536.
12. Arnold, H. H.,, and G. Keith. 1977. The nucleotide sequence of phenylalanine tRNA from Bacillus subtilis. Nucleic Acids Res. 4:28212822.
13. Arnold, H. H.,, R. Raettig,, and G. Keith. 1977. Isoaccepting phenylalanine tRNAs from Bacillus subtilis as a function of growth conditions. Differences in the content of modified nucleosides. FEBS Lett. 73:210214.
14. Arps, P. J.,, C. C. Marvel,, B. C. Rubin,, D. A. Tolan,, E. E. Penhoet,, and M. E. Winkler. 1985. Structural features of the hisT operon of Escherichia coli K-12. Nucleic Acids Res. 13:52975315.
15. Arps, P. J.,, and M. E. Winkler. 1987. Structural analysis of the Escherichia coli K-12 hisT operon by using a kanamycin resistance cassette. J. Bacterial. 169:10611070.
16. Aschhoff, H. J.,, H. Elten,, H. H. Arnold,, G. Mahal,, W. Kersten,, and H. Kersten. 1976. 7-methylguanine specific tRNA-methyltransferase from Escherichia coli. Nucleic Acids Res. 3:31093122.
16a. Aström, S. U.,, and A. S. Bystrom. Personal communication.
17. Atkins, J. F.,, R. B. Weiss,, S. Thompson,, and R. F. Gesteland. 1991. Towards a genetic dissection of the basis of triplet decoding, and its natural subversion: programmed reading frame shifts and hops. Annu. Rev. Genet. 25:201228.
18. Bacha, H.,, M. Renaud,, J.-F. Lefevre,, and P. Remy. 1982. Conformational activation of aminoacyl-tRNA synthetases upon binding of tRNA. A facet of a multi-step adaptation process leading to the optimal biological acitivity. Eur. J. Biochem. 127:8795.
19. Bare, L. A.,, and O. C. Uhlenbeck. 1986. Specific substitution into the anticodon loop of yeast tyrosine transfer RNA. Biochemistry 25:58255830.
20. Bartz, J. K.,, L. K. Kline,, and D. Soil. 1970. N6-(2-isopen-tenyl)adenosine: biosynthesis in vitro in transfer RNA by an enzyme purified from Escherichia coli. Biochem. Biophys. Res. Commun. 40:14811487.
21. Bartz, J. K.,, D. Soli,, W. J. Burrows,, and F. Skoog. 1970. Identification of the cytokinin-active ribonucleosides in pure Escherichia coli tRNA species. Proc. Natl. Acad. Sci. USA 67:14481453.
22. Beck, C. F.,, and R. A. J. Warren. 1988. Divergent promoters, a common form of gene organization. Microbiol. Rev. 52:318326.
23. Beier, H.,, M. Barciszewska,, G. Krupp,, R. Mitnacht,, and H. J. Gross. 1984. UAG readthrough during TMV RNA translation: isolation and sequence of two tRNAsTyr with suppressor activity from tobacco plants. EMBO J. 3:351356.
24. Beier, H.,, M. Barciszewska,, and H.-D. Sickinger. 1984. The molecular basis for the differential translation of TMV RNA in tobacco protoplasts and wheat germ extracts. EMBO J. 3:10911096.
25. Beier, H.,, U. Zech,, E. Zubrod,, and H. Kersten. 1987. Queuine in plants and plant tRNAs: differences between embryonic tissue and mature leaves. Plant Mol. Biol. 8:345353.
26. Bell-Pedersen, D.,, J. L. Galloway Salvo,, and M. Belfort. 1991. A transcription terminator in the thymidylate synthetase (thyA) structural gene of Escherichia coli and construction of a viable thyA::Kmr deletion. J. Bacterial. 173:11931200.
27. Bienz, M.,, and E. Kubli. 1981. Wild-type tRNATyrG reads the TMV RNA stop codon, but Q base-modified tRNATyrQ does not. Nature (London) 294:188190.
28. Björk, G. R. 1975. Identification of bacteriophage T4-specific precursor tRNA by using a host mutant defective in the methylation of tRNA. J. Virol. 16:741744.
29. Björk, G. R. 1975. Transductional mapping of gene trmA responsible for the production of 5-methyluridine in transfer RNA of Escherichia coli. J. Bacteriol. 124:9298.
30. Björk, G. R. 1980. A novel link between the biosynthesis of aromatic amino acids and transfer RNA modification in Escherichia coli. J. Mol. Biol. 140:391410.
31. Björk, G. R. 1984. Transfer RNA modification in different organisms. Chemica Scripta 26B:9195.
32. Björk, G. R., 1987. Modification of stable RNA, p. 719731. 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, vol. 1. American Society for Microbiology, Washington, D.C.
33. Björk, G. R., 1992. The role of modified nucleosides in tRNA interactions, p. 23D85D. In L. Hatfield,, B. J. Lee,, and R. M. Pirtle, (ed.), Transfer RNA in Protein Synthesis. CRC Press, Boca Raton, Fla.
34. Björk, G. R.,, J. U. Ericson,, C. E. D. Gustafsson,, T. G. Hagervall,, Y. H. Jonsson,, and P. M. Wikström. 1987. Transfer RNA modification. Annu. Rev. Biochem. 56:263287.
35. Björk, G. R.,, and I. Svensson. 1969. Studies on microbiological RNA. Fractionation of tRNA methylases from Saccharomyces cerevisiae. Eur. ]. Biochem. 9:207215.
36. Björk, G. R.,, P. M. Wikström,, and A. S. Bystrom. 1989. Prevention of translational frameshifting by the modified nucleoside 1-methylguanosine. Science 244:986989.
37. Bochner, B. R.,, D. L. Lee,, S. W. Wilson,, C. W. Cutter,, and B. N. Ames. 1984. AppppA and related adenylated nucleotides are synthesized as a consequence of oxidation stress. Cell 37:225232.
38. Bognar, A. L.,, C. Osborne,, and B. Shane. 1987. Primary structure of the Escherichia coli folC gene and its folylpolyglutamate synthetase-dihydrofolate synthetase product and regulation of expression by upstream gene. J. Biol. Chem. 262:1233712343.
39. Bognar, A.,, C. Pyne,, M. Yu,, and G. Basi. 1989. Transcription of the folC gene encoding folylpolyglutamate synthetase-dihydrofolate synthetase in Escherichia coli. J. Bacteriol. 171:18541861.
40. Borek, E.,, A. Ryan,, and J. Rockenbach. 1955. Nucleic acid metabolism in relation to the lysogeneic phenomenon. J. Bacteriol. 69:460467.
41. Borén, T.,, P. Elias,, T. Samuelsson,, C. Claesson,, M. Barciszewska,, C. W. Gehrke,, K. C. Kuo,, and F. Lustig. 1993. Undiscriminating codon reading with adenosine in wobble position.J. Mol. Biol. 230:739749.
42. Boy, E.,, F. Borne,, and J.-C. Patte. 1978. Effect of mutations affecting lysyl-tRNALys on the regulation of lysine biosynthesis in Escherichia coli. Mol. Gen. Genet. 159:3338.
43. Breitenberger, C. A.,, and U. L. RajBhandary. 1985. Some highlights of mitochondrial research based on analyses of Neurospora crassa mitochondrial DNA. Trends Biochem. Sci. 10:478483.
44. Brenchley, J. E.,, and L. S. Williams. 1975. Transfer RNA involvement in the regulation of enzyme synthesis. Annu. Rev. Microbiol. 29:251274.
45. Bresalier, R. S.,, A. A. Rizzino,, and M. Freundlich. 1975. Reduced maximal levels of derepression of the isoleucinevaline and leucine enzymes in hisT mutant of Salmonella typhimurium. Nature (London) 253:279280.
46. Bruni, C. B.,, V. Colantuoni,, L. Sbordone,, R. Cortese,, and F. Blasi. 1977. Biochemical and regulatory properties of Escherichia coli K-12 hisT mutants. J. Bacteriol. 130:410.
46a. Buck, M. Personal communication.
47. Buck, M.,, and B. N. Ames. 1984. A modified nucleotide in tRNA as a possible regulator of aerobiosis: synthesis of cis-2-methyl-thioribosyslzeatin in tRNA of Salmonella. Cell 36:523531.
48. Buck, M.,, M. Connick,, and B. N. Ames. 1983. Complete analysis of tRNA-modified nucleosides by high-performanceliquid chromatography: the 29 modified nucleosides of Salmonella typhimurium and Escherichia coli tRNA. Anal.Biol. Chem.129:113.
49. Buck, M.,, and E. Griffiths. 1981. Regulation of aromatic amino acid transport by tRNA: role of 2-methylthio-N6-(2-isopentenyl)-adenosine. Nucleic Acids Res. 9:401414.
50. Buck, M.,, and E. Griffiths. 1982. Iron mediated methylthiolation of tRNA as a regulator of operon expression in Escherichia coli. Nucleic Acids Res. 10:26092624.
51. Buck, M.,, J. A. McCloskey,, B. Basile,, and B. N. Ames. 1982. Cis-2-methylthio-ribosylzeatin (ms2io6A) is present in transfer RNA of Salmonella typhimurium, but not Escherichia coli. Nucleic Acids Res. 10:56495662.
52. Buu, A.,, B. Menichi,, and T. Heyman. 1981. Thiomethylation of tyrosine ribonucleic acid is associated with initiation of sporulation in Bacillus subtilis: effect of phosphate concentration. J. Bacteriol. 146:819822.
53. Byström, A. S.,, and G. R. Björk. 1982. Chromosomal location and cloning of the gene (trmD) responsible for the synthesis of tRNA(m1G)methyltransferase in Escherichia coli K-12. Mol. Gen. Genet. 188:440446.
54. Byström, A. S.,, K. J. Hjalmarsson,, P. M. Wikström,, and G. R. Björk. 1983. The nucleotide sequence of an Escherichia coli operon containing genes for the tRNA(m1G) methyltransferase, the ribosomal proteins S16 and L19 and a 21-K polypeptide. EMBO J. 2:899905.
55. Bystrom, A. S.,, A. von Gabain,, and G. R. Björk. 1989. Differentially expressed trmD ribosomal protein operon of Escherichia coli is transcribed as a single polycistronic mRNA species. J. Mol. Biol. 208:575586.
56. Caillet, J.,, and L. Droogmans. 1988. Molecular cloning of the Escherichia coli miaA gene involved in the formation of 2-isopentenyl adenosine in tRNA. J. Bacteriol. 170:41474152.
57. Caldeira de Araujo, A.,, and A. Favre. 1986. Near ultraviolet DNA damage induces the SOS responses in Escherichia coli. EMBO J. 5:175179.
58. Carbon, J.,, and E. W. Fleck. 1974. Genetic alteration of structure and function in glycine transfer RNA of Escherichia coli: mechanism of suppression of the tryptophan synthetase A78 mutation. J. Mol. Biol. 85:371391.
59. Carbon, P.,, E. Haumont,, M. Fournier,, S. de Henau,, and H. Grosjean. 1983. Site-directed in vitro replacement of nucleosides in the anticodon loop of tRNA: application to the study of structural requirements for queuine insertase activity. EMBO J. 2:10931097.
60. Cashel, M.,, and Rudd, K. E., 1987. The stringent response, p. 14101438. 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, vol. 2. American Society for Microbiology, Washington, D.C.
61. Cheung, P. K.,, and M. B. Herrington. 1982. Thymine inhibits suppression by an Escherichia coli nonsense and frameshift suppressor. Mol. Gen. Genet. 186:217220.
62. Chheda, G. B.,, C. I. Hong,, C. F. Piskorz,, and G. A. Harmon. 1972. Biosynthesis of N-(purin-6-ylcarbamoyl)-L-threonine riboside. Incorporation of L-threonine in vivo into modified nucleoside of transfer ribonucleic acid. Biochem. J. 127:515519.
63. Ching, W.-M.,, B. Alzner-DeWeerd,, and T. C. Stadtman. 1985. A selenium-containing nucleotide at the first position of the anticodon in seleno-tRNAGln from Clostridium stick-landii. Proc. Natl. Acad. Sci. USA 82:347350.
64. Ching, W.-M.,, and T. S. Stadtman. 1982. Selenium-containing tRNAGlu from Clostridium sticklandii: correlation of aminoacylation with selenium content. Proc. Natl. Acad. Sci. USA 79:374377.
65. Ching, W.-M.,, L. Tsai,, and A. J. Witwer. 1985. Selenium containing transfer RNAs. Curr. Top. Cell. Regul. 27:497507.
66. Choffat, Y.,, B. Suter,, R. Behra,, and E. Kubli. 1988. Pseudouridine modification in the tRNATyr anticodon is dependent on the presence, but independent of the size and sequence, of the intron in eucaryotic tRNATyr genes. Mol. Cell. Biol. 8:33323337.
67. Chow, C. S.,, L. S. Behlen,, O. C. Uhlenbeck,, and J. K. Barton. 1992. Recognition of tertiary structure in tRNAs by Rh(phen)2phi3 +, a new reagent for RNA structure-function mapping. Biochemistry 31:972982.
68. Ciampi, M. S.,, F. Arena,, and R. Cortese. 1977. Biosynthesis of pseudouridine in the in vitro transcribed tRNATyr precursor. FEBS Lett. 77:7582.
69. Ciliberto, G.,, L. Castagnoli,, and R. Cortese. 1983. Transcription by RNA polymerase III. Curr. Top. Dev. Biol. 18:5988.
70. Clarkson, S. G., 1983. Transfer RNA genes, p. 239261. In G. S. P. McLean, and R. A. Flavell (ed.), Eukaryotic Genes: Their Structure, Activity and Regulation. Butterworths, London.
71. Conlon-Hollingshead, C.,, and B. J. Ortwerth. 1980. Lys-tRNA4 levels and cell division in mouse 3T3 cells. Exp. Cell Res. 128:171180.
72. Connolly, D. M.,, and M. E. Winkler. 1989. Genetic and physiological relationships among the miaA genes, 2-meth-ylthio-N6-(2-isopentenyl)-adenosine tRNA modification, and spontaneous mutagenesis in Escherichia coli K-12. J. Bacterial. 171:32333246.
73. Connolly, D. M.,, and M. E. Winkler. 1991. Structure of Escherichia coli K-12 miaA and characterization of the mutator phenotype caused by miaA insertion mutations. J. Bacterial. 173:17111721.
74. Cortese, R.,, H. O. Kammen,, S. J. Spengler,, and B. N. Ames. 1974. Biosynthesis of pseudouridine in transfer ribonucleic acid. J. Biol. Chem. 249:11031108.
75. Cortese, R.,, R. Landsberg,, R. A. Vonder Haar,, H. E. Umbarger,, and B. N. Ames. 1974. Pleitropy of hisT mutants blocked in pseudouridine synthesis in tRNA: leucine and isoleucine-valine operons. Proc. Natl. Acad. Sci. USA. 71:18571861.
76. Crick, F. C. H. 1966. Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol. 19:548555.
77. Curnow, A. W.,, F.-L. Rung,, K. A. Koch,, and G. A. Garcia. 1993. tRNA-Guanine transglycosylase from Escherichia coli: gross tRNA structural requirements for recognition. Biochemistry 32:52395246.
78. Davis, A. R.,, and D. P. Nierlich. 1974. The methylation of transfer RNA in Escherichia coli. Biochim. Biophys. Acta 374:2337.
79. Del Carmen Rodríguez-Sáinz, M.,, C. Hernández-Chico,, and F. Moreno. 1991. A hisT::Tn5 mutation affects production of microcins B17, C7, and H47 and colicin V. J. Bacterial. 173:70187020.
80. Delk, A. S.,, D. P. Nagle, Jr.,, and J. C. Rabinowitz,. 1979. The methylenetetrahydrofolate-dependent biosynthesis of ribothymidine in the transfer-RNA of Streptococcus faecalis, p. 389394. In R. L. Kisliuk, and G. M. Brown (ed.), Chemistry and Biology of Pteridines. Elsevier/North Holland, Inc., Amsterdam.
81. Delk, A. S.,, D. P. Nagle, Jr.,, and J. C. Rabinowitz. 1980. Methylentetrahydrofolate-dependent biosynthesis of ribothymidine in transfer RNA of Streptococcus faecalis. J. Biol. Chem. 255:43874390.
82. Delk, A. S.,, and J. C. Rabinowitz. 1975. Biosynthesis of ribosylthymine in the tRNA of Strepococcus faecalis: a folate-dependent methylation not involving S-ade-nosylmethionine. Proc. Natl. Acad. Sci. USA 72:528530.
83. Delk, A. S.,, J. M. Romeo,, D. P. Nagle, Jr.,, and J. C. Rabinowitz. 1976. Biosynthesis of ribothymidine in the transfer RNA of Streptococcus faecalis and Bacillus subtilis. A methylation of RNA involving 5,10-methylenetetrahydrofolate. J. Biol. Chem. 251:76497656.
84. DeRobertis, E. M.,, and K. Nishikura,. 1981. RNA processing in frog oocytes microinjected with cloned genes, p. 6065. In H. G. Schweiger (ed.), International Cell Biology. Springer-Verlag, Berlin.
85. Deutscher, M. P. 1985. Processing of tRNA in prokaryotes and eukaryotes. Crit. Rev. Biochem. 17:4571.
86. Dickson, R. R.,, T. Gaal,, H. A. deBoer,, P. L. deHaseth,, and R. L. Gourse. 1989. Identification of promoter mutants defective in growth-rate-dependent regulation of rRNA transcription in Escherichia coli. J. Bacterial 171:48624870.
87. Dihanich, M. E.,, D. Majarian,, R. Clark,, E. C. Gillman,, N. C. Martin,, and A. K. Hopper. 1987. Isolation and characterization of MOD5, a gene required for isopentenylation of cytoplasmic and mitochondrial tRNAs of Saccharomyces cerevisiae. Mol. Cell. Biol. 7:177184.
88. Dirheimer, G. 1983. Chemical nature, properties, location, and physiological and pathological variations of modified nucleosides in tRNA. Recent Results Cancer Res. 84:1546.
89. Droogmans, L.,, and H. Grosjean. 1987. Enzymatic conversion of guanosine 3' adjacent to the anticodon of yeast tRNAPhe to N1-methylguanosine and the wye nucleoside: dependence on the anticodon sequence. EMBO J. 6:477483.
90. Droogmans, L.,, and H. Grosjean. 1991. 2'-0-methylation and inosine formation in the wobble position of anticodonsubstituted tRNAphe in a homologous in vitro system. Biochimie 73:10211025.
91. Droogmans, L.,, E. Haumont,, S. de Henau,, and H. Grosjean. 1986. Enzymatic 2'-0-methylation of the wobble nucleoside of eukaryotic tRNAphe: specificity depends on structural elements outside the anticodon loop. EMBO J. 5:11051109.
92. Dube, S. K.,, K. A. Marker,, B. F. C. Clark,, and S. Cory. 1968. Nucleotide sequence of N-formyl-methionyl-transfer RNA. Nature (London) 218:232233.
93. Dugré, M.,, and R. J. Cedergren. 1973. Origine de l'inosine dans les tRNA de levure. Can. J. Biochem. 52:417422.
94. Dunn, D. B. 1959. Additional components in ribonucleic acid of rat-liver fractions. Biochim. Biophys. Acta 34:286288.
95. Edmonds, C. G.,, P. F. Crain,, R. Gupta,, T. Hashizume,, C. H. Hocart,, J. A. Kowalak,, S. C. Pomerantz,, K. O. Stetter,, and J. A. McCloskey. 1991. Posttranscriptional modification of tRNA in thermophilic Archaea (Archaebacteria). J. Bacteriol. 173:31383148.
96. Edqvist J.,, H. Grosjean,, and K. B. Straby. 1993. Identity elements for N2-dimethylation of guanosine-26 in yeast tRNAs. Nucleic Acids Res. 20:65756581.
97. Edqvist, J.,, and K. B. Straby. 1992. The recognition between a yeast tRNA(dimethyl G26)methyltransferase and its homologous yeast tRNA substrate. 16th International Conference on Yeast Genetics and Molecular Biology, p. 204.
98. Edqvist, J.,, K. B. Straby,, and H. Grosjean. 1993. Pleiotrophic effects of point mutations in yeast tRNAAsp on the base modification pattern. Nucleic Acids Res. 21:413417.
99. Ehrenreich, A.,, K. Forchhammer,, P. Tormay,, B. Veprek,, and A. Böck. 1992. Selenoprotein synthesis in E. coli. Purification and characterisation of the enzyme catalysing selenium activation. Eur. J. Biochem. 206:767773.
100. Eisenberg, S. P.,, M. Yarus,, and L. Soil. 1979. The effect of an Escherichia coli regulatory mutation on transfer RNA structure. J. Mol. Biol. 135:111126.
101. Elkins, B. N.,, and E. B. Keller. 1974. The enzymatic synthesis of N-(purin-6-ylcarbamoyl)threonine, an anticodon-adjacent base in transfer ribonucleic acid. Biochemistry 13:46224628.
102. Elliott, M. S.,, J. R. Katze,, and R. W. Trewyn. 1984. Relationship between a tumor promoter-induced decrease in queuine modification of transfer RNA in normal and human cells and the expression of an altered cell phenotype. Cancer Res. 44:32153219.
103. Elliott, M. S.,, and R. W. Trewyn. 1984. Inosine biosynthesis in transfer RNA by an enzymatic insertion of hypoxanthine. J. Biol. Chem. 259:24072410.
104. Elliott, M. S.,, R. W. Trewyn,, and J. R. Katze. 1985. Inhibition of queuine uptake in cultured human fibroblasts by phorbol-12,13-didecanoate. Cancer Res. 45:10791085.
105. Ellis, S. R.,, A. K. Hopper,, and N. C. Martin. 1987. Amino-terminal extension generated from an upstream AUG codon is not required for mitochondrial import of yeast N2,N2-dimethylguanosine-specific tRNA methyltransferase. Proc. Natl. Acad. Sci. USA. 84:51725176.
106. Ellis, S. R.,, A. K. Hopper,, and N. C. Martin. 1989. Amino-terminal extension generated from an upstream AUG codon increases the efficiency of mitochondrial import of yeast N2,N2-dimethylguanosine-specific tRNA methyltransferase. Mol. Cell. Biol. 9:16111620.
107. Ellis, S. R.,, M. J. Morales,, J.-M. Li,, A. K. Hopper,, and N. C. Martin. 1986. Isolation and characterization of the TRM1 locus, a gene essential for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNA in Saccharomyces cerevisae. J. Biol. Chem. 261:97039709.
108. Elseviers, D.,, L. A. Petrullo,, and P. J. Gallagher. 1984. Novel E. coli mutants deficient in biosynthesis of 5-meth-ylaminomethyl-2-thiouridine. Nucleic Acids Res. 12:35213534.
109. Emilsson, V.,, and C. G. Kurland. 1990. Growth rate dependence of transfer RNA abundance in Escherichia coli. EMBO J. 9:43594366.
110. Emilsson, V.,, A. K. Naslund,, and C. G. Kurland. 1992. Thiolation of transfer RNA in Escherichia coli varies with growth rate. Nucleic Acids Res. 20:44994505.
111. Engelberg-Kulka, H.,, and R. Schonlaker-Schwarz. 1988. Stop is not the end: physiological implications of translational readthrough. J. Theor. Biol. 131:477485.
112. Ericson, J. U.,, and G. R. Björk. 1986. Pleiotropic effects induced by modification deficiency next to the anticodon of tRNA from Salmonella typhimurium LT2. J. Bacteriol. 166:10131021.
112a. Esberg, B.,, and G. R. Björk. Unpublished data.
113. Etcheverry, T.,, D. Colby,, and C. Guthrie. 1979. A precursor to a minor species of yeast tRNASer contains an intervening sequence. Cell 18:1126.
114. Farkas, W. R.,, and R. D. Singh. 1973. Guanylation of transfer ribonucleic acid by a cell-free lysate of rabbit reticulocytes. J. Biol. Chem. 248:77807785.
115. Fasiolo, F.,, T. Glade,, G. Keith,, V. Buttcher,, F. Cramer,, and U. Englisch. 1993. The codon and amino acid specificity of the yeast isoleucine transfer RNAs are dependent on two distinct modified wobble bases, p. 76. 15th International tRNA Workshop.
116. Faulkner, R. D.,, and M. Uziel. 1971. Iodine modification of E. coli tRNAphe: reversible modification of 2-methylthio-N6-isopentenyladenosine and lack of disulfide formation. Biochim. Biophys. Acta 238:464474.
117. Favre, A.,, E. Hajnsdorf,, K. -Thiam,, and A. Caldeira de Araujo. 1985. Mutagenesis and growth delay induced in Escherichia coli by near-ultraviolet radiations. Biochimie 67:335342.
118. Favre, A.,, M. Yaniv,, and A. M. Michelson. 1969. The photochemistry of 4-thiouridine in Escherichia coli tRNAval1. Biochem. Biophys. Res. Commun. 37:266271.
119. Fayerman, J. F.,, M. C. Vann,, L. S. Williams,, and H. E. Umbarger. 1979. ilvU, a locus in Escherichia coli affecting the derepression of isoleucyl-tRNA synthetase and the RPC-5 chromatographic profiles of tRNAIle and tRNAVal. J. Biol. Chem. 254:94299440.
120. Fittler, F.,, L. K. Kline,, and R. H. Hall. 1968. Biosynthesis of N6-(2-isopentenyl) adenosine. Precursor relationship of acetate and mevalonate to the 2-isopentenyl group of the transfer ribonucleic acid of microorganisms. Biochemistry 7:940944.
121. Fittler, F.,, L. K. Kline,, and R. H. Hall. 1968. N6-(2-isopentenyljadenosine: biosynthesis in vitro by an enzyme extract from yeast and rat liver. Biochem. Biophys. Res. Commun. 31:571576.
122. Fleissner, E.,, and E. Borek. 1962. A new enzyme of RNA synthesis: RNA methylase. Proc. Natl. Acad. Sci. USA 48:11991203.
123. Fournier, M. J.,, E. Webb,, and G. R. Kitchingman. 1976. General and specific effects of amino acid starvation on the formation of undermodified Escherichia coli phenylalanine tRNA. Biochem. Biophys. Acta 454:97113.
124. French, B. T.,, D. E. Patrick,, M. G. Grever,, and R. W. Trewyn. 1991. Queuine, a tRNA anticodon wobble base, maintains the proliferative and pluripotent potential of HL-60 cell in the presence of the differentiating agent 6-thioguanine. Proc. Natl. Acad. Sci. USA 88:370374.
125. Frey, B.,, G. Jänel,, U. Michelsen,, and H. Kersten. 1989. Mutations in the Escherichia coli fnr and tgt genes: control of molybdate reductase activity and the cytochrome d complex by fnr.J. Bacteriol. 171:15241530.
126. Frey, B.,, J. McCloskey,, W. Kersten,, and H. Kersten. 1988. New function of vitamin B12: cobamide-dependent reduction of epoxyqueuosine to queuosine in tRNAs of Escherichia coli and Salmonella typhimurium. J. Bacteriol. 170:20782082.
127. Gaal, X.,, J. Barkei,, R. R. Dickson,, H. A. deBoer,, P. L. deHaseth,, H. Alavi,, and R. L. Gourse. 1989. Saturation mutagenesis of an Escherichia coli rRNA promoter and initial characterization of promoter variants. J. Bacteriol. 171:48524861.
128. Gallagher, P. J.,, I. Schwartz,, and D. Elseviers. 1984. Genetic mapping of pheU, an Escherichia coli gene for phenylalanine tRNA. J. Bacteriol. 158:762763.
129. Garcia, A. 1990. Thesis. Université Louis Pasteur, Strasbourg, France.
130. Gefter, M. L. 1969. The in vitro synthesis of 2'-meth-ylguanosine and 2-methylthio 6N(λ,λ, dimethylallyl) adenosine in transfer RNA of Escherichia coli. Biochem. Biophys. Res. Commun. 36:435441.
131. Gefter, M. L.,, and R. L. Russel. 1969. Role of modifications in tyrosine transfer RNA: a modified base affecting ribosome binding. J. Mol. Biol. 39:145157.
131a. Gehrke, C. Personal communication.
132. Giegé, R. A.,, J. D. Puglisi,, and C. Florentz. 1993. tRNA structure and aminoacylation efficiency. Prog. Nucleic Acid Mol. Biol. 45:129206.
133. Gillman, E. C.,, L. B. Slusher,, N. C. Martin,, and A. K. Hopper. 1991. MOD5 translation initiation sites determine N6-isopentenyladenosine modification of mitochondrial and cytoplasmic tRNA. Mol. Cell. Biol. 11:23822390.
134. Glasser, A.-L.,, C. E. Adlouni,, G. Keith,, E. Sochacka,, E. Malkiewicz,, M. Santos,, M. F. Tuite,, and J. Degres. 1992. Presence and coding properties of 2'-O-methyl-5-carbamoylmethyluridine (ncm5Um) in the wobble position of the anticodon of tRNALeu (U*AA) from brewer's yeast. FEBS Lett. 314:381385.
135. Glick, J. M.,, V. M. Averyhart,, and P. S. Leboy. 1978. Purification and characterization of two tRNA-(guanine)-methyltransferases from rat liver. Biochem. Biophys. Acta 518:158171.
136. Glick, J. M.,, and P. S. Leboy. 1977. Purification and properties of tRNA(adenine-l) methyltransferase from rat liver. J. Biol. Chem. 252:47904795.
137. Glick, J. M.,, S. Ross,, and P. S. Leboy. 1975. S-adenosylhomocysteine inhibition of three purified tRNA methyltransferases from rat liver. Nucleic Acids Res. 2:16391651.
138. Goddard, J. P.,, and M. Lowdon. 1981. The effect upon aminoacylation of bisulphite addition to 2-methylthio-N6-isopentenyl adenosine of Escherichia coli phenylalanine tRNA. FEBS Lett. 130:221222.
139. Goldstein, J. L.,, and M. Brown. 1990. Regulation of the mevalonate pathway. Nature (London) 343:425430.
140. Gray, J.,, J. Wang,, and S. B. Gelvin. 1992. Mutation of the miaA gene of Agrobacterium tumefaciens results in reduced vir gene expression. J. Bacteriol. 174:10861098.
141. Greenberg, R.,, and B. Dudock. 1980. Isolation and characterization of m5U-methyltransferase from Escherichia coli. J. Biol. Chem. 255:82968302.
142. Griffey, R. H.,, D. Davis,, Z. Yamaizumi,, S. Nishimura,, A. Bax,, B. Hawkins,, and C. D. Poulter. 1985. 15N-labeled Escherichia coli tRNAMetf, tRNAGlu, tRNATyr, and tRNAphe. Double resonance and two-dimensional NMR of N1-labeled pseudouridine. J. Biol. Chem. 260:97349741.
143. Griffiths, E.,, and J. Humphreys. 1978. Alterations in tRNAs containing 2-methylthio-N6-2-isopentenyl)-adenosine during growth of enteropathogenic Escherichia coli in the presence of iron-binding proteins. Eur. J. Biochem. 82:503513.
143a. Grosjean, H. Personal communication.
144. Grosjean, H.,, S. de Henau,, T. Doi,, A. Yamane,, E. Ohtsuka,, M. Ikehara,, N. Beauchemin,, K. Nicoghosian,, and R. Cedergren. 1987. The in vivo stability, maturation and aminoacylation of anticodon-substituted Escherichia coli initiator methionine tRNAs. Eur. J. Biochem. 166:325332.
145. Grosjean, H.,, L. Droogmans,, R. Giege,, and O. Uhlenbeck. 1990. Guanosine modifications in runoff transcripts of synthetic transfer RNA-Phe genes microinjected into Xenopus oocytes. Biochem Biophys. Acta 1050:267273.
146. Grosjean, H.,, E. Haumont,, L. Droogmans,, P. Carbon,, M. Fournier,, S. de Henau,, T. Doi,, G. Keith,, J. Gangloff,, K. Kretz,, and R. Trewyn,. 1987. A novel approach to the biosynthesis of modified nucleosides in the anticodon loops of eukaryotic transfer RNAs, p. 355378. In K. S. Bruzik, and W. J. Stec (ed.), Biophosphates and Their Analogues: Synthesis, Structure, Metabolism and Activity. Elsevier, Amsterdam.
147. Grosjean, H.,, and C. Houssier. 1990. Codon recognition: evaluation of the effects of modified bases in the anticodon loop of tRNA using the temperature-jump relaxation method. J. Chromatogr. Library 45A:A255A295.
148. Grosjean, H.,, G. Keith,, and C. Houssier. 1984. Anticodon-anticodon interactions: evaluation of the effect of 2'-O-methyl modification to ribose of cytosine-34 in yeast tRNATrp. Arch. Int. Physiol. Biochem. 92:B137.
149. Grosjean, H.,, K. Nicoghosian,, E. Haumont,, D. Söil,, and R. Cedergren. 1985. Nucleotide sequences of two serine tRNAs with a GGA anticodon: the structure-function relationships in the serine family of E. coli tRNAs. Nucleic Acids Res. 13:56975706.
150. Grossenbacher, A.-M.,, J. Kohli,, K. C. Kuo,, and C. W. Gehrke. 1990. Synthesis and function of modified nucleosides in tRNA. In Chromatograpy and modification of nucleosides. Part B. Biological roles and function of modification. J. Chromatogr. Library 45B:B13B67.
151. Grossenbacher, A.-M.,, B. Stadelman,, W.-D. Heyer,, P. Thuriaux,, and J. Kohli. 1986. Antisuppressor mutations and sulfur-carrying nucleosides in transfer RNAs of Schizosac-charomyces pombe. J. Biol. Chem. 261:1635116355.
152. Gu, X.,, and D. V. Santi. 1990. High-level expression of Escherichia coli tRNA (m5U54)methyltransferase. DNA and Cell Biol. 9:273278.
153. Gu, X.,, and D. V. Santi. 1991. The T-arm of tRNA is a substrate for tRNA(m5U54)-methyltransferase. Biochemistry 30:29993002.
154. Gu, X.,, and D. V. Santi. 1992. Covalent adducts between tRNA(m5U54)-methyltransferase and RNA substrates. Biochemistry 31:1029510302.
155. Gustafsson, C. 1992. Ph.D. thesis. Umea University.
156. Gustafsson, C.,, and G. R. Björk. 1993. The tRNA-(m5U54)-methyltransferase of Escherichia coli is present in two forms in vivo, one of which is covalently bound to tRNA and to a 3'-end fragment of 16S rRNA. J. Biol. Chem. 268:13261331.
157. Gustafsson, C.,, P. H. R. Lindström,, T. G. Hagervall,, K. B. Esberg,, and G. R. Bjork. 1991. The trmA promoter has regulatory features and sequence elements in common with the rRNA PI promoter familly in Escherichia coli. J. Bacteriol. 173:17571764.
157a. Hagervall, T.,, and J. McCloskey. Personal communication.
158. Hagervall, T. G.,, and G. R. Bjork. 1984. Undermodification in the first position of the anticodon of swpG-tRNA reduces translational efficiency. Mol. Gen. Genet. 196:194200.
159. Hagervall, T. G.,, and G. R. Björk. 1984. Genetic mapping and cloning of the gene (trmC) responsible for the synthesis of tRNA(mnm5s2U)methyltransferase in Escherichia coli K12. Mol. Gen. Genet. 196:201207.
160. Hagervall, T. G.,, C. G. Edmonds,, J. A. McCloskey,, and G. R. Bjork. 1987. Transfer RNA(5-methylaminomethyl-2-thiouridine)methyltransferase from Escherichia coli K-12 has two enzymatic activities. J. Biol. Chem. 262:84888495.
161. Hagervall, T. G.,, Y. H. Jönsson,, C. G. Edmonds,, J. A. McCloskey,, and G. R. Björk. 1990. Chorismic acid, a key metabolite in modification of tRNA. J. Bacteriol. 172:252259.
162. Hagervall, T. G.,, T. M. Tuohy,, J. F. Atkins,, and G. R. Bjork. 1993. Deficiency of 1-methylguanosine in tRNA from Salmonella typhimurium induces frameshifting by quadruplet translocation.J. Mol. Biol. 232:756765.
163. Hall, K. B.,, J. R. Sampson,, O. C. Uhlenbeck,, and A. G. Redfield. 1989. Structure of an unmodified tRNA molecule. Biochemistry 28:57945801.
164. Hall, R. H. 1970. N6-(2-isopentenyl)adenosine: chemical reactions, biosynthesis, metabolism, and significance to the structure and function of tRNA. Prog. Nucleic Acids Res. Mol. Biol. 10:5786.
165. Hall, R. H. 1971. The Modified Nucleosides in Nucleic Acids. Columbia University Press, New York.
166. Harada, R.,, and S. Nishimura. 1972. Possible anticodon sequences of tRNAHis, tRNAAsn, and tRNAAsp from Escherichia coli B. Universal presence of nucleoside Q in the first position of the anticodons of these transfer ribonucleic acids. Biochemistry 11:301308.
167. Harris, C. L. 1990. High-molecular-weight forms of amino-acyl-tRNA synthetases and tRNA modifying enzymes in Escherichia coli. J. Bacteriol. 172:17981803.
168. Harris, C. L.,, K. Marin,, and D. Stewart. 1977. tRNA sulfurtransferase: a member of the aminoacyl-tRNA synthetase complex in rat liver. Biochem. Biophys. Res. Commun. 79:657662.
169. Hasegawa, T.,, M. Miyano,, H. Himeno,, Y. Sano,, K. Kimura,, and M. Shimizu. 1992. Identity determinants of E. coli threonine tRNA. Biochem. Biophys. Res. Commun. 184:478484.
170. Hatfield, D. L.,, J. G. Levin,, A. Rein,, and S. Oroszlan. 1992. Translational suppression in retroviral gene expression. Adv. Virus Res. 41:193239.
171. Hatfield, D. L.,, D. W. E. Smith,, B. J. Lee,, P. J. Worland,, and S. Oroszlan. 1990. Structure and function of suppressor tRNAs in higher eukaryotes. Crit. Rev. Biochem. Mol. Biol. 25:7196.
172. Haumont, E.,, L. Droogmans,, and H. Grosjean. 1987. Enzymatic formation of queuosine and of glycerol queuosine in yeast tRNA microinjected into Xenopus laevis oocytes. The effect of the anticodon loop sequence. Eur. J. Biochem. 168:219225.
173. Haumont, E.,, M. Fournier,, S. deHenau,, and H. Grosjean. 1984. Enzymatic conversion of adenosine to inosine in the wobble position of yeast tRNAAsp: the dependence on the anticodon sequence. Nucleic Acids Res. 12:27052715.
174. Hecht, S. M.,, L. H. Kirkegaard,, and R. M. Bock. 1971. Chemical modifications of transfer RNA species. Desulfurization with raney nickel. Proc. Natl. Acad. Sci. USA 68:4851.
175. Herrington, M. B.,, J. Basso,, M. Farci,, and C. Autexier. 1991. Modification of the suppressor phenotype of thymine requiring strains of Escherichia coli. Genet. Res. 58:18592.
176. Herrington, M. B.,, A. Kohli,, and P. H. Lapchak. 1984. Suppression by thymidine-requiring mutants of Escherichia coli K-12.J. Bacteriol. 157:126129.
177. Heyer, W.-D.,, P. Thuriaux,, and J. Kohli. 1984. An antisup-pressor mutation of Schizosaccharomyuces pombe affects the post-transcriptional modification of the "Wobble" base in the anticodon of tRNAs. J. Biol. Chem. 259:28562862.
178. Hilderman, R. H.,, and B. J. Ortwerth. 1987. A preferential role for lysyl-tRNA4 in the synthesis of diadenosine 5',5'-P1,P4-tetraphosphate by an arginyl-tRNA-lysyl-tRNA synthetase complex from rat liver. Biochemistry 26:15861591.
179. Hjalmarsson, K. J.,, A. Byström,, and G. R. Björk. 1983. Purification and characterization of transfer RNA(Guanine-1 )methyltransferase from Escherichia coli. J. Biol. Chem. 258:13431351.
180. Hoagland, M. E.,, P. C. Zamecnik,, and M. L. Stephenson. 1957. Intermediate reactions in protein synthesis. Biochim. Biophys. Acta 24:215216.
181. Holmes, W. M.,, C. Andraos-Selim,, I. Roberts,, and S. Z. Wahab. 1992. Structural requirements for tRNA methylation. Action of Escherichia coli tRNA(guanosine-1) methyltransferase on tRNALeu1 structural variants. J. Biol. Chem. 267:1344013445.
182. Hopper, A. K.,, A. H. Furukawa,, H. D. Pham,, and N. C. Martin. 1982. Defects in modification of cytoplasmic and mitochondrial transfer RNAs are caused by single nuclear mutations. Cell 28:543550.
183. Hori, H.,, M. Saneyoshi,, I. Kumagai,, K.-I. Miura,, and K. Watanabe. 1989. Effects of modification of 4-thiouridine in E. coli tRNAMetf on its methyl acceptor activity by thermostable Gm-methylases. J. Biochem. 106:798802.
184. Hotchkiss, R. D. 1948. The quantitative separation of purines, pyrimidines, and nucleosides by paper chromatography. J. Biol. Chem. 175:315332.
185. Houssier, C.,, P. Degree,, K. Nicoghosian,, and H. Grosjean. 1988. Effect of uridine dethiolation in the anticodon triplet of tRNA (Glu) on its association with tRNA (Phe). J. Biol. Mol. Struct. Dyn. 5:12591266.
186. Ivanetich, K. M.,, and D. V. Santi. 1992. 5,6,-Dihydropyrimidine adducts in the reactions and interactions of pyrimidines with proteins. Prog. Nucleic Acids Res. Mol. Biol. 42:127156.
187. Jagger, J. 1983. Physiological effects of near-ultraviolet radiation on bacteria. Photochem. Photobiol. Rev. 7:173.
188. Janner, E.,, G. Vdgeli,, and R. Fluri. 1980. The antisuppressor strain sinl of Schizosaccharomyces pombe lacks the modification isopentenyladenosine in transfer RNA. J. Mol. Biol. 139:207219.
189. Jensen, K. F. 1993. The Escherichia coli K-13 "wild type" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. J. Bacteriol. 175:34013407.
190. Jeter, R. M.,, B. M. Olivera,, and J. R. Roth. 1984. Salmonella typhimurium synthesizes cobalamin (vitamin B12) de novo under unaerobic growth conditions. J. Bacteriol. 159:206213.
191. Johnson, P. F.,, and J. Abelson. 1983. The yeast tRNATyr gene intron is essential for correct modification of its tRNA product. Nature (London) 302:681687.
192. Johnson, R.,, and M. L. Simon. 1985. Hin-mediated site-specific recombination requires two 26 bp recombination sites and a 60 bp recombinational enhancer. Cell 41:781791.
193. Jukes, T. H. 1973. Possibility for the evolution of the genetic code from a preceding form. Nature (London) 246:2226.
194. Kadner, R. J. 1978. Repression of synthesis of the vitamin B12 receptor in Escherichia coli. J. Bacterial. 136:10501057.
195. Kahmann, R. F.,, F. Rudt,, C. Koch,, and G. Marlens. 1985. G inversion in bacteriophage Mu DNA is stimulated by a site within the inverstase gene and a host factor. Cell 41:771780.
196. Kajitani, M.,, and A. Ishihama. 1991. Identification and sequence determination of the host factor gene for bacteriophage Q. Nucleic Acids Res. 19:10631066.
197. Kammen, H. O.,, C. C. Marvel,, L. Hardy,, and E. E. Penhoet. 1988. Purification, structure, and properties of Escherichia coli tRNA pseudouridine synthase. J. Biol. Chem. 263:22552263.
198. Kammen, H. O.,, and S. J. Spengler. 1970. The biosynthesis of inosinic acid in transfer RNA. Biochem. Biophys. Acta 213:352364.
199. Kane, S. M.,, C. Vugrinicic,, D. S. Finbloom,, and D. W. E. Smith. 1978. Purification and some properties of the histidyl-tRNA synthetase from the cytosol of rabbit reticulocytes. Biochemistry 17:15091514.
200. Kang, H. S.,, R. C. Ogden,, G. Knapp,, C. L. Peebles,, and J. Abelson,. 1979. Structure of yeast tRNA precursors containing intervening sequences, p. 6984. In R. Axel,, T. Maniatis,, and E. Fox (ed.), Eucaryotic Gene Regulation. Academic Press, Inc., New York.
201. Katze, J. R.,, M. H. Simonian,, and R. D. Mosteller. 1977. Role of methionine in the synthesis of nucleoside Q in Escherichia coli transfer RNA. J. Bacteriol. 132:174179.
202. Kawai, G.,, Y. Yamamoto,, T. Kamimura,, T. Masegi,, M. Sekine,, T. Hata,, T. Iimori,, T. Watanabe,, T. Miyazawa,, and S. Yokoyama. 1992. Conformational rigidity of specific pyrimidine residues in tRNA arises from posttranscriptional modifications that enhance steric interaction between the base and the 2'-hydroxyl group. Biochemistry 31:10401046.
203. Kawakami, K.,, Y. H. Jönsson,, G. R. Björk,, H. Ikeda,, and Y. Nakamura. 1988. Chromosomal location and structure of the operon encoding peptide-chain-release factor 2 of Escherichia coli. Proc. Natl. Acad. Sci. USA 85:56205624.
204. Kealey, J. X.,, S. Lee,, H. G. Floss,, and D. V. Santi. 1991. Sterochemistry of methyl transfer catalyzed by tRNA(m5U54)methyltransferase — evidence of a single displacement mechanism. Nucleic Acids Res. 23:64656468.
205. Kealey, J. T.,, and D. V. Santi. 1991. Identification of the catalytic nucleophile of tRNA(m5U54)methyltransferase. Biochemistry 30:97249728.
206. 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. 61:120123.
207. Keith, J. M.,, E. M. Winters,, and B. Moss. 1980. Purification and characterization of a HeLa cell transfer RNA-(cytosine-5)-methyltransferase. J. Biol. Chem. 255:46364644.
208. Kern, D.,, and J. Lapointe. 1979. Glutamyl transfer ribonucleic acid synthetase of Escherichia coli. Effect of alteration of the 5-(methylaminomethyl)-2-thiouridine in the anticodon of glutamic acid transfer ribonucleic acid on the catalytic mechanism. Biochemistry 18:58195826.
209. Kersten, H. 1984. On the biological significance of modified nucleosides in tRNA. Prog. Nucleic Acids Res. Mol. Biol. 31:58114.
210. Kersten, H. 1988. The nutrient factor queuine: biosynthesis, occurrence in transfer RNA and function. Biofactors 1:2729.
211. Kersten, H.,, and W. Kersten. 1990. Biosynthesis and function of queuine and queuosine tRNAs. In Chromatography and modification of nucleosides. Part B. Biological roles and function of modification. J. Chromatogr. Library 45B:B69B108.
212. Kersten, H.,, R. Raettig,, J. Weissenbach,, and G. Dirheimer. 1978. Recognition of individual procaryotic and eucaryotic transfer-ribonucleic acids by B. subtilis adenine-l-meth-yltransferase specific for the dihydrouridine loop. Nucleic Acids Res. 5:30333042.
213. Kersten, H.,, L. Sandig,, and H. H. Arnold. 1975. Tetrahydrofolate-dependent 5-methyluracil-tRNA transferase activity in B. subtilis. FEBS Lett. 55:5760.
214. Kitchingman, G. R.,, and M. J. Fournier. 1975. Unbalanced growth and the production of unique transfer ribonucleic acids in relaxed-control Escherichia coli. J. Bacteriol. 124:13821394.
215. Kitchingman, G. R.,, and M. J. Fournier. 1976. In vivo maturation of an undermodified Escherichia coli leucine transfer RNA Biochem. Biophys. Res. Commun. 73:314322.
216. Kitchingman, G. R.,, and M. J. Fournier. 1977. Modification-deficient transfer ribonucleic acids from relaxed control Escherichia coli: structures of the major undermodified phenylalanine and leucine transfer RNAs produced during leucine starvation. Biochemistry 16:22132220.
217. Kline, L. K.,, F. Fittler,, and R. H. Hall. 1969. N6-(2-isopen-tenyl)adenosine. Biosynthesis in transfer ribonucleic acid in vitro. Biochemistry 8:43614371.
218. 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. 212:579598.
219. Körner, A.,, and D. Söll. 1974. N-(purin-6-ylcarbamoyl)-threonine: biosynthesis in vitro in transfer RNA by an enzyme purified from Escherichia coli. FEBS Lett. 39:301306.
220. Kowalak, J. A.,, and J. A. McCloskey,. 1992. The determination of posttranscriptional modification in RNA, p. 7988. In K. Nierhaus (ed.), Translational Apparatus. Springer-Verlag, Berlin.
221. Kramer, G. F.,, and B. N. Ames. 1988. Isolation and characterization of a selenium metabolism mutant of Salmonella typhimurium. J. Bacteriol. 170:736743.
222. Kramer, G. E.,, J. C. Baker,, and B. N. Ames. 1988. Near-UV stress in Salmonella typhimurium: 4-thiouridine in tRNA, ppGpp, and ApppGpp as components of and adaptive response.J. Bacteriol. 170:2344