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. 1984 Apr 25;12(8):3521–3534. doi: 10.1093/nar/12.8.3521

Novel E. coli mutants deficient in biosynthesis of 5-methylaminomethyl-2-thiouridine.

D Elseviers, L A Petrullo, P J Gallagher
PMCID: PMC318766  PMID: 6427754

Abstract

Novel E. coli mutants deficient in biosynthesis of 5- methylaminomethyl -2-thiouridine were isolated based on a phenotype of reduced readthrough at UAG codons. They define 2 new loci trmE and trmF , near 83' on the E. coli map. These mutants are different from strains carrying trmC mutations, which are known to confer a methylation deficiency in biosynthesis of 5- methylaminomethyl -2-thiouridine. tRNA from mutants carrying trmE or trmF mutations was shown to carry 2-thiouridine instead of 5- methylaminomethyl -2-thiouridine. This deficiency affects the triplet binding properties of the mutant tRNA. Our results suggest that the 5- methylaminomethyl group stabilizes the basepairing of this modified nucleotide with G, most likely through direct interaction with the ribosomal binding site(s).

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  1. Agris P. F., Söll D., Seno T. Biological function of 2-thiouridine in Escherichia coli glutamic acid transfer ribonucleic acid. Biochemistry. 1973 Oct 23;12(22):4331–4337. doi: 10.1021/bi00746a005. [DOI] [PubMed] [Google Scholar]
  2. Björk G. R., Kjellin-Stråby K. Escherichia coli mutants with defects in the biosynthesis of 5-methylaminomethyl-2-thio-uridine or 1-methylguanosine in their tRNA. J Bacteriol. 1978 Feb;133(2):508–517. doi: 10.1128/jb.133.2.508-517.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Borck K., Beggs J. D., Brammar W. J., Hopkins A. S., Murray N. E. The construction in vitro of transducing derivatives of phage lambda. Mol Gen Genet. 1976 Jul 23;146(2):199–207. doi: 10.1007/BF00268089. [DOI] [PubMed] [Google Scholar]
  4. Borer P. N., Dengler B., Tinoco I., Jr, Uhlenbeck O. C. Stability of ribonucleic acid double-stranded helices. J Mol Biol. 1974 Jul 15;86(4):843–853. doi: 10.1016/0022-2836(74)90357-x. [DOI] [PubMed] [Google Scholar]
  5. Bossi L., Ruth J. R. The influence of codon context on genetic code translation. Nature. 1980 Jul 10;286(5769):123–127. doi: 10.1038/286123a0. [DOI] [PubMed] [Google Scholar]
  6. Capecchi M. R. Polypeptide chain termination in vitro: isolation of a release factor. Proc Natl Acad Sci U S A. 1967 Sep;58(3):1144–1151. doi: 10.1073/pnas.58.3.1144. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Chakraburtty K., Steinschneider A., Case R. V., Mehler A. H. Primary structure of tRNA-Lys of E. coli B. Nucleic Acids Res. 1975 Nov;2(11):2069–2075. doi: 10.1093/nar/2.11.2069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Chang A. C., Cohen S. N. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J Bacteriol. 1978 Jun;134(3):1141–1156. doi: 10.1128/jb.134.3.1141-1156.1978. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Chang G. W., Roth J. R., Ames B. N. Histidine regulation in Salmonella typhimurium. 8. Mutations of the hisT gene. J Bacteriol. 1971 Oct;108(1):410–414. doi: 10.1128/jb.108.1.410-414.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Crick F. H. Codon--anticodon pairing: the wobble hypothesis. J Mol Biol. 1966 Aug;19(2):548–555. doi: 10.1016/s0022-2836(66)80022-0. [DOI] [PubMed] [Google Scholar]
  11. Deeley M. C., Yanofsky C. Nucleotide sequence of the structural gene for tryptophanase of Escherichia coli K-12. J Bacteriol. 1981 Sep;147(3):787–796. doi: 10.1128/jb.147.3.787-796.1981. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Donohue J. On N-H--S hydrogen bonds. J Mol Biol. 1969 Oct 28;45(2):231–235. doi: 10.1016/0022-2836(69)90102-8. [DOI] [PubMed] [Google Scholar]
  13. Elseviers D., Gallagher P., Hoffman A., Weinberg B., Schwartz I. Molecular cloning and regulation of expression of the genes for initiation factor 3 and two aminoacyl-tRNA synthetases. J Bacteriol. 1982 Oct;152(1):357–362. doi: 10.1128/jb.152.1.357-362.1982. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Elseviers D., Gorini L. Direct selection of mutants restricting efficiency of suppression and misreading levels in E. coli B. Mol Gen Genet. 1975;137(4):277–287. doi: 10.1007/BF00703254. [DOI] [PubMed] [Google Scholar]
  15. Folk W. R., Yaniv M. Coding properties and nucleotide sequences of E. coli glutamine tRNAs. Nat New Biol. 1972 Jun 7;237(75):165–166. doi: 10.1038/newbio237165a0. [DOI] [PubMed] [Google Scholar]
  16. Fuller W., Hodgson A. Conformation of the anticodon loop intRNA. Nature. 1967 Aug 19;215(5103):817–821. doi: 10.1038/215817a0. [DOI] [PubMed] [Google Scholar]
  17. Gauss D. H., Sprinzl M. Compilation of tRNA sequences. Nucleic Acids Res. 1983 Jan 11;11(1):r1–53. [PMC free article] [PubMed] [Google Scholar]
  18. Gefter M. L., Russell R. L. Role modifications in tyrosine transfer RNA: a modified base affecting ribosome binding. J Mol Biol. 1969 Jan 14;39(1):145–157. doi: 10.1016/0022-2836(69)90339-8. [DOI] [PubMed] [Google Scholar]
  19. Gorini L. The contrasting role of strA and ram gene products in ribosomal functioning. Cold Spring Harb Symp Quant Biol. 1969;34:101–109. doi: 10.1101/sqb.1969.034.01.016. [DOI] [PubMed] [Google Scholar]
  20. Grosjean H. J., de Henau S., Crothers D. M. On the physical basis for ambiguity in genetic coding interactions. Proc Natl Acad Sci U S A. 1978 Feb;75(2):610–614. doi: 10.1073/pnas.75.2.610. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Guthrie C., Seidman J. G., Altman S., Barrell B. G., Smith J. D., McClain W. H. Identification of tRNA precursor molecules made by phage T4. Nat New Biol. 1973 Nov 7;246(149):6–11. doi: 10.1038/newbio246006a0. [DOI] [PubMed] [Google Scholar]
  22. Hillen W., Egert E., Lindner H. J., Gassen H. G. Restriction or amplification of wobble recognition: the structure of 2-thio-5-methylaminomethyluridine and the interaction of odd uridines with the anticodon loop backbone. FEBS Lett. 1978 Oct 15;94(2):361–364. doi: 10.1016/0014-5793(78)80977-6. [DOI] [PubMed] [Google Scholar]
  23. KAISER A. D., HOGNESS D. S. The transformation of Escherichia coli with deoxyribonucleic acid isolated from bacteriophage lambda-dg. J Mol Biol. 1960 Dec;2:392–415. doi: 10.1016/s0022-2836(60)80050-2. [DOI] [PubMed] [Google Scholar]
  24. Marinus M. G., Morris N. R., Söll D., Kwong T. C. Isolation and partial characterization of three Escherichia coli mutants with altered transfer ribonucleic acid methylases. J Bacteriol. 1975 Apr;122(1):257–265. doi: 10.1128/jb.122.1.257-265.1975. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Mazumdar S. K., Saenger W. Molecular structure of poly-2-thiouridylic acid, a double helix with non-equivalent polynucleotide chains. J Mol Biol. 1974 May 15;85(2):213–219. doi: 10.1016/0022-2836(74)90361-1. [DOI] [PubMed] [Google Scholar]
  26. Miki T., Hiraga S., Nagata T., Yura T. Bacteriophage lambda carrying the Escherichia coli chromosomal region of the replication origin. Proc Natl Acad Sci U S A. 1978 Oct;75(10):5099–5103. doi: 10.1073/pnas.75.10.5099. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Müller W., Crothers D. M. Interactions of heteroaromatic compounds with nucleic acids. 1. The influence of heteroatoms and polarizability on the base specificity of intercalating ligands. Eur J Biochem. 1975 May;54(1):267–277. doi: 10.1111/j.1432-1033.1975.tb04137.x. [DOI] [PubMed] [Google Scholar]
  28. NIRENBERG M., LEDER P. RNA CODEWORDS AND PROTEIN SYNTHESIS. THE EFFECT OF TRINUCLEOTIDES UPON THE BINDING OF SRNA TO RIBOSOMES. Science. 1964 Sep 25;145(3639):1399–1407. doi: 10.1126/science.145.3639.1399. [DOI] [PubMed] [Google Scholar]
  29. Neidhardt F. C., Bloch P. L., Smith D. F. Culture medium for enterobacteria. J Bacteriol. 1974 Sep;119(3):736–747. doi: 10.1128/jb.119.3.736-747.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Oashi Z., Saneyoshi M., Harada F., Hara H., Nishimura S. Presumed anticodon structure of glutamic acid tRNA from E. coli: a possible location of a 2-thiouridine derivative in the first position of the anticodon. Biochem Biophys Res Commun. 1970 Aug 24;40(4):866–872. doi: 10.1016/0006-291x(70)90983-6. [DOI] [PubMed] [Google Scholar]
  31. Petrullo L. A., Gallagher P. J., Elseviers D. The role of 2-methylthio-N6-isopentenyladenosine in readthrough and suppression of nonsense codons in Escherichia coli. Mol Gen Genet. 1983;190(2):289–294. doi: 10.1007/BF00330653. [DOI] [PubMed] [Google Scholar]
  32. Rogg H., Brambilla R., Keith G., Staehelin M. An improved method for the separation and quantitation of the modified nucleosides of transfer RNA. Nucleic Acids Res. 1976 Jan;3(1):285–295. doi: 10.1093/nar/3.1.285. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Schaefler S., Maas W. K. Inducible system for the utilization of beta-glucosides in Escherichia coli. II. Description of mutant types and genetic analysis. J Bacteriol. 1967 Jan;93(1):264–272. doi: 10.1128/jb.93.1.264-272.1967. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Thomas M., Davis R. W. Studies on the cleavage of bacteriophage lambda DNA with EcoRI Restriction endonuclease. J Mol Biol. 1975 Jan 25;91(3):315–328. doi: 10.1016/0022-2836(75)90383-6. [DOI] [PubMed] [Google Scholar]
  35. Timmis K. N., Cabello F., Cohen S. N. Cloning and characterization of EcoRI and HindIII restriction endonuclease-generated fragments of antibiotic resistance plasmids R6-5 and R6. Mol Gen Genet. 1978 Jun 14;162(2):121–137. doi: 10.1007/BF00267869. [DOI] [PubMed] [Google Scholar]
  36. VOGEL H. J., BONNER D. M. Acetylornithinase of Escherichia coli: partial purification and some properties. J Biol Chem. 1956 Jan;218(1):97–106. [PubMed] [Google Scholar]
  37. Vormbrock R., Morawietz R., Gassen H. G. Codon-anticodon interaction studies with trinucleoside diphosphates containing 2-thiouridine, 4-thiouridine, 2,4-diethiouridine, or 2-thiocytidine. Biochim Biophys Acta. 1974 Mar 27;340(3):348–358. [PubMed] [Google Scholar]
  38. Yanofsky C. Mutations affecting tRNATrp and its charging and their effect on regulation of transcription termination at the attenuator of the tryptophan operon. J Mol Biol. 1977 Jul 15;113(4):663–677. doi: 10.1016/0022-2836(77)90229-7. [DOI] [PubMed] [Google Scholar]
  39. Yarus M. Translational efficiency of transfer RNA's: uses of an extended anticodon. Science. 1982 Nov 12;218(4573):646–652. doi: 10.1126/science.6753149. [DOI] [PubMed] [Google Scholar]

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