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. 1992 May 1;89(9):3995–3998. doi: 10.1073/pnas.89.9.3995

The gene for a tRNA modifying enzyme, m5U54-methyltransferase, is essential for viability in Escherichia coli.

B C Persson 1, C Gustafsson 1, D E Berg 1, G R Björk 1
PMCID: PMC525618  PMID: 1373891

Abstract

One of the most abundant modified nucleosides in tRNA is 5-methyluridine (m5U or rT, ribothymidine). The enzyme tRNA(m5U54)methyltransferase [S-adenosyl-L-methionine:tRNA (uracil-5-)-methyltransferase, EC 2.1.1.35] (the trmA gene product) catalyzes S-adenosylmethionine-dependent methylation of the uracil in position 54 (T psi C loop) in all Escherichia coli tRNAs to form m5U. Hitherto no modified nucleoside in tRNA has been shown to be essential for growth, although their importance in fine tuning the function of tRNA is well established. In this paper, we show that the structural gene trmA is essential for viability, although the known catalytic activity of the tRNA(m5U54)methyltransferase is not.

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Selected References

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  1. Andachi Y., Yamao F., Muto A., Osawa S. Codon recognition patterns as deduced from sequences of the complete set of transfer RNA species in Mycoplasma capricolum. Resemblance to mitochondria. J Mol Biol. 1989 Sep 5;209(1):37–54. doi: 10.1016/0022-2836(89)90168-x. [DOI] [PubMed] [Google Scholar]
  2. Anderson P., Roth J. Spontaneous tandem genetic duplications in Salmonella typhimurium arise by unequal recombination between rRNA (rrn) cistrons. Proc Natl Acad Sci U S A. 1981 May;78(5):3113–3117. doi: 10.1073/pnas.78.5.3113. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. BERTANI G. Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol. 1951 Sep;62(3):293–300. doi: 10.1128/jb.62.3.293-300.1951. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Björk G. R., Ericson J. U., Gustafsson C. E., Hagervall T. G., Jönsson Y. H., Wikström P. M. Transfer RNA modification. Annu Rev Biochem. 1987;56:263–287. doi: 10.1146/annurev.bi.56.070187.001403. [DOI] [PubMed] [Google Scholar]
  5. Björk G. R., Isaksson L. A. Isolation of mutants of Escherichia coli lac king 5-methyluracil in transfer ribonucleic acid or 1-methylguanine in ribosomal RNA. J Mol Biol. 1970 Jul 14;51(1):83–100. doi: 10.1016/0022-2836(70)90272-x. [DOI] [PubMed] [Google Scholar]
  6. Björk G. R., Neidhardt F. C. Evidence for the utilization of host tRNA(m 5 U)methylase to modify tRNA coded by phage T4. Virology. 1973 Apr;52(2):507–519. doi: 10.1016/0042-6822(73)90346-2. [DOI] [PubMed] [Google Scholar]
  7. Björk G. R., Neidhardt F. C. Physiological and biochemical studies on the function of 5-methyluridine in the transfer ribonucleic acid of Escherichia coli. J Bacteriol. 1975 Oct;124(1):99–111. doi: 10.1128/jb.124.1.99-111.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Björk G. R. Transductional mapping of gene trmA responsible for the production of 5-methyluridine in transfer ribonucleic acid of Escherichia coli. J Bacteriol. 1975 Oct;124(1):92–98. doi: 10.1128/jb.124.1.92-98.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Casadaban M. J., Cohen S. N. Analysis of gene control signals by DNA fusion and cloning in Escherichia coli. J Mol Biol. 1980 Apr;138(2):179–207. doi: 10.1016/0022-2836(80)90283-1. [DOI] [PubMed] [Google Scholar]
  10. Davanloo P., Sprinzl M., Watanabe K., Albani M., Kersten H. Role of ribothymidine in the thermal stability of transfer RNA as monitored by proton magnetic resonance. Nucleic Acids Res. 1979 Apr;6(4):1571–1581. doi: 10.1093/nar/6.4.1571. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Feinberg A. P., Vogelstein B. "A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity". Addendum. Anal Biochem. 1984 Feb;137(1):266–267. doi: 10.1016/0003-2697(84)90381-6. [DOI] [PubMed] [Google Scholar]
  12. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  13. Gu X. R., Santi D. V. The T-arm of tRNA is a substrate for tRNA (m5U54)-methyltransferase. Biochemistry. 1991 Mar 26;30(12):2999–3002. doi: 10.1021/bi00226a003. [DOI] [PubMed] [Google Scholar]
  14. Guindy Y. S., Samuelsson T., Johansen T. I. Unconventional codon reading by Mycoplasma mycoides tRNAs as revealed by partial sequence analysis. Biochem J. 1989 Mar 15;258(3):869–873. doi: 10.1042/bj2580869. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gustafsson C., Lindström P. H., Hagervall T. G., Esberg K. B., Björk G. R. The trmA promoter has regulatory features and sequence elements in common with the rRNA P1 promoter family of Escherichia coli. J Bacteriol. 1991 Mar;173(5):1757–1764. doi: 10.1128/jb.173.5.1757-1764.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hagervall T. G., Edmonds C. G., McCloskey J. A., Björk G. R. Transfer RNA(5-methylaminomethyl-2-thiouridine)-methyltransferase from Escherichia coli K-12 has two enzymatic activities. J Biol Chem. 1987 Jun 25;262(18):8488–8495. [PubMed] [Google Scholar]
  17. Hopper A. K., Furukawa A. H., Pham H. D., Martin N. C. Defects in modification of cytoplasmic and mitochondrial transfer RNAs are caused by single nuclear mutations. Cell. 1982 Mar;28(3):543–550. doi: 10.1016/0092-8674(82)90209-4. [DOI] [PubMed] [Google Scholar]
  18. Johnson L., Hayashi H., Söll D. Isolation and properties of a transfer ribonucleic acid deficient in ribothymidine. Biochemistry. 1970 Jul 7;9(14):2823–2831. doi: 10.1021/bi00816a011. [DOI] [PubMed] [Google Scholar]
  19. Kealey J. T., Santi D. V. Identification of the catalytic nucleophile of tRNA (m5U54)methyltransferase. Biochemistry. 1991 Oct 8;30(40):9724–9728. doi: 10.1021/bi00104a022. [DOI] [PubMed] [Google Scholar]
  20. Kersten H., Albani M., Männlein E., Praisler R., Wurmbach P., Nierhaus K. H. On the role of ribosylthymine in prokaryotic tRNA function. Eur J Biochem. 1981 Feb;114(2):451–456. doi: 10.1111/j.1432-1033.1981.tb05166.x. [DOI] [PubMed] [Google Scholar]
  21. Kohara Y., Akiyama K., Isono K. The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell. 1987 Jul 31;50(3):495–508. doi: 10.1016/0092-8674(87)90503-4. [DOI] [PubMed] [Google Scholar]
  22. Komine Y., Adachi T., Inokuchi H., Ozeki H. Genomic organization and physical mapping of the transfer RNA genes in Escherichia coli K12. J Mol Biol. 1990 Apr 20;212(4):579–598. doi: 10.1016/0022-2836(90)90224-A. [DOI] [PubMed] [Google Scholar]
  23. Kulakauskas S., Wikström P. M., Berg D. E. Efficient introduction of cloned mutant alleles into the Escherichia coli chromosome. J Bacteriol. 1991 Apr;173(8):2633–2638. doi: 10.1128/jb.173.8.2633-2638.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Lindström P. H., Stüber D., Björk G. R. Genetic organization and transcription from the gene (trmA) responsible for synthesis of tRNA (uracil-5)-methyltransferase by Escherichia coli. J Bacteriol. 1985 Dec;164(3):1117–1123. doi: 10.1128/jb.164.3.1117-1123.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Marcu K. B., Dudock B. S. Effect of ribothymidine in specific eukaryotic tRNAs on their efficiency in in vitro protein synthesis. Nature. 1976 May 13;261(5556):159–162. doi: 10.1038/261159a0. [DOI] [PubMed] [Google Scholar]
  26. Pang H., Ihara M., Kuchino Y., Nishimura S., Gupta R., Woese C. R., McCloskey J. A. Structure of a modified nucleoside in archaebacterial tRNA which replaces ribosylthymine. 1-Methylpseudouridine. J Biol Chem. 1982 Apr 10;257(7):3589–3592. [PubMed] [Google Scholar]
  27. Rayssiguier C., Thaler D. S., Radman M. The barrier to recombination between Escherichia coli and Salmonella typhimurium is disrupted in mismatch-repair mutants. Nature. 1989 Nov 23;342(6248):396–401. doi: 10.1038/342396a0. [DOI] [PubMed] [Google Scholar]
  28. Roe B. A., Tsen H. Y. Role of ribothymidine in mammalian tRNAPhe. Proc Natl Acad Sci U S A. 1977 Sep;74(9):3696–3700. doi: 10.1073/pnas.74.9.3696. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Samuelsson T., Guindy Y. S., Lustig F., Borén T., Lagerkvist U. Apparent lack of discrimination in the reading of certain codons in Mycoplasma mycoides. Proc Natl Acad Sci U S A. 1987 May;84(10):3166–3170. doi: 10.1073/pnas.84.10.3166. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Singer M., Baker T. A., Schnitzler G., Deischel S. M., Goel M., Dove W., Jaacks K. J., Grossman A. D., Erickson J. W., Gross C. A. A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol Rev. 1989 Mar;53(1):1–24. doi: 10.1128/mr.53.1.1-24.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Vani B. R., Ramakrishnan T., Taya Y., Noguchi S., Yamaizumi Z., Nishimura S. Occurrence of 1-methyladenosine and absence of ribothymidine in transfer ribonucleic acid of Mycobacterium smegmatis. J Bacteriol. 1979 Mar;137(3):1084–1087. doi: 10.1128/jb.137.3.1084-1087.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Wikström P. M., Byström A. S., Björk G. R. Non-autogenous control of ribosomal protein synthesis from the trmD operon in Escherichia coli. J Mol Biol. 1988 Sep 5;203(1):141–152. doi: 10.1016/0022-2836(88)90098-8. [DOI] [PubMed] [Google Scholar]
  33. Winans S. C., Elledge S. J., Krueger J. H., Walker G. C. Site-directed insertion and deletion mutagenesis with cloned fragments in Escherichia coli. J Bacteriol. 1985 Mar;161(3):1219–1221. doi: 10.1128/jb.161.3.1219-1221.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]

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