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. 1992 Mar;174(6):1956–1964. doi: 10.1128/jb.174.6.1956-1964.1992

Expression of argU, the Escherichia coli gene coding for a rare arginine tRNA.

P Saxena 1, J R Walker 1
PMCID: PMC205802  PMID: 1548236

Abstract

The Escherichia coli argU gene encodes the rare arginine tRNA, tRNA(UCUArg), which decodes the similarly rare AGA codons. The argU promoter is, with two exceptions, a typical, strongly expressed stable RNA gene promoter which is stimulated by an upstream activator sequence. Unlike other tRNA operons, however, argU expression is severely inhibited by sequences downstream of the transcription start point. In vivo, nucleotides +2 to +45 inhibited expression by 25- to 100-fold when measured by fusion of argU promoter regions to the chloramphenicol acetyltransferase reporter gene or by quantitative primer extension analysis. In vitro, linearized argU promoter fragments on which the argU region ended at +1 supported 5- to 10-fold-more transcription than when the argU region ended at +45. This difference in degree of inhibition between in vivo and in vitro conditions suggests that several factors, some of which could be absent in vitro, might limit expression in vivo. Alternatively, one mechanism might limit expression both in vivo and in vitro but function more efficiently in vivo. A second difference from strongly expressed stable RNA promoters is the fact the argU gene is relatively insensitive to growth rate regulation, at least when assayed on a multicopy plasmid.

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Selected References

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  1. An G., Friesen J. D. The nucleotide sequence of tufB and four nearby tRNA structural genes of Escherichia coli. Gene. 1980 Dec;12(1-2):33–39. doi: 10.1016/0378-1119(80)90013-x. [DOI] [PubMed] [Google Scholar]
  2. Aota S., Gojobori T., Ishibashi F., Maruyama T., Ikemura T. Codon usage tabulated from the GenBank Genetic Sequence Data. Nucleic Acids Res. 1988;16 (Suppl):r315–r402. doi: 10.1093/nar/16.suppl.r315. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Bossi L., Smith D. M. Conformational change in the DNA associated with an unusual promoter mutation in a tRNA operon of Salmonella. Cell. 1984 Dec;39(3 Pt 2):643–652. doi: 10.1016/0092-8674(84)90471-9. [DOI] [PubMed] [Google Scholar]
  4. Bradford M. M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem. 1976 May 7;72:248–254. doi: 10.1006/abio.1976.9999. [DOI] [PubMed] [Google Scholar]
  5. Brosius J. Plasmid vectors for the selection of promoters. Gene. 1984 Feb;27(2):151–160. doi: 10.1016/0378-1119(84)90136-7. [DOI] [PubMed] [Google Scholar]
  6. Celis T. F., Maas W. K. Studies on the mechanism of repression of arginine biosynthesis in Escherichia coli. IV. Further studies on the role of arginine transfer RNA repression of the enzymes of arginine biosynthesis. J Mol Biol. 1971 Nov 28;62(1):179–188. doi: 10.1016/0022-2836(71)90138-0. [DOI] [PubMed] [Google Scholar]
  7. Chen E. Y., Seeburg P. H. Supercoil sequencing: a fast and simple method for sequencing plasmid DNA. DNA. 1985 Apr;4(2):165–170. doi: 10.1089/dna.1985.4.165. [DOI] [PubMed] [Google Scholar]
  8. Chen K. S., Peters T. C., Walker J. R. A minor arginine tRNA mutant limits translation preferentially of a protein dependent on the cognate codon. J Bacteriol. 1990 May;172(5):2504–2510. doi: 10.1128/jb.172.5.2504-2510.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Danchin A., Dondon L. Regulatory features of tRNA Leu I expression in Escherichia coli K12. Biochem Biophys Res Commun. 1979 Oct 29;90(4):1280–1286. doi: 10.1016/0006-291x(79)91175-6. [DOI] [PubMed] [Google Scholar]
  10. Dickson R. R., Gaal T., deBoer H. A., deHaseth P. L., Gourse R. L. Identification of promoter mutants defective in growth-rate-dependent regulation of rRNA transcription in Escherichia coli. J Bacteriol. 1989 Sep;171(9):4862–4870. doi: 10.1128/jb.171.9.4862-4870.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Duester G., Campen R. K., Holmes W. M. Nucleotide sequence of an Escherichia coli tRNA (Leu 1) operon and identification of the transcription promoter signal. Nucleic Acids Res. 1981 May 11;9(9):2121–2139. doi: 10.1093/nar/9.9.2121. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Duester G., Elford R. M., Holmes W. M. Fusion of the Escherichia coli tRNALeu1 promoter to the galK gene: analysis of sequences necessary for growth-rate-dependent regulation. Cell. 1982 Oct;30(3):855–864. doi: 10.1016/0092-8674(82)90290-2. [DOI] [PubMed] [Google Scholar]
  13. Emilsson V., Kurland C. G. Growth rate dependence of transfer RNA abundance in Escherichia coli. EMBO J. 1990 Dec;9(13):4359–4366. doi: 10.1002/j.1460-2075.1990.tb07885.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Fournier M. J., Ozeki H. Structure and organization of the transfer ribonucleic acid genes of Escherichia coli K-12. Microbiol Rev. 1985 Dec;49(4):379–397. doi: 10.1128/mr.49.4.379-397.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Gaal T., Barkei J., Dickson R. R., deBoer H. A., deHaseth P. L., Alavi H., Gourse R. L. Saturation mutagenesis of an Escherichia coli rRNA promoter and initial characterization of promoter variants. J Bacteriol. 1989 Sep;171(9):4852–4861. doi: 10.1128/jb.171.9.4852-4861.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Garcia G. M., Mar P. K., Mullin D. A., Walker J. R., Prather N. E. The E. coli dnaY gene encodes an arginine transfer RNA. Cell. 1986 May 9;45(3):453–459. doi: 10.1016/0092-8674(86)90331-4. [DOI] [PubMed] [Google Scholar]
  17. Gourse R. L., de Boer H. A., Nomura M. DNA determinants of rRNA synthesis in E. coli: growth rate dependent regulation, feedback inhibition, upstream activation, antitermination. Cell. 1986 Jan 17;44(1):197–205. doi: 10.1016/0092-8674(86)90498-8. [DOI] [PubMed] [Google Scholar]
  18. Gouy M., Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 1982 Nov 25;10(22):7055–7074. doi: 10.1093/nar/10.22.7055. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Harley C. B., Reynolds R. P. Analysis of E. coli promoter sequences. Nucleic Acids Res. 1987 Mar 11;15(5):2343–2361. doi: 10.1093/nar/15.5.2343. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Hawley D. K., McClure W. R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res. 1983 Apr 25;11(8):2237–2255. doi: 10.1093/nar/11.8.2237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Hudson L., Rossi J., Landy A. Dual function transcripts specifying tRNA and mRNA. Nature. 1981 Dec 3;294(5840):422–427. doi: 10.1038/294422a0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Hübner P., Arber W. Mutational analysis of a prokaryotic recombinational enhancer element with two functions. EMBO J. 1989 Feb;8(2):577–585. doi: 10.1002/j.1460-2075.1989.tb03412.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol. 1981 Feb 15;146(1):1–21. doi: 10.1016/0022-2836(81)90363-6. [DOI] [PubMed] [Google Scholar]
  24. Ishii S., Ihara M., Maekawa T., Nakamura Y., Uchida H., Imamoto F. The nucleotide sequence of the cloned nusA gene and its flanking region of Escherichia coli. Nucleic Acids Res. 1984 Apr 11;12(7):3333–3342. doi: 10.1093/nar/12.7.3333. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Ishii S., Kuroki K., Imamoto F. tRNAMetf2 gene in the leader region of the nusA operon in Escherichia coli. Proc Natl Acad Sci U S A. 1984 Jan;81(2):409–413. doi: 10.1073/pnas.81.2.409. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Johnson R. C., Simon M. I. Hin-mediated site-specific recombination requires two 26 bp recombination sites and a 60 bp recombinational enhancer. Cell. 1985 Jul;41(3):781–791. doi: 10.1016/s0092-8674(85)80059-3. [DOI] [PubMed] [Google Scholar]
  27. Kahmann R., Rudt F., Koch C., Mertens G. G inversion in bacteriophage Mu DNA is stimulated by a site within the invertase gene and a host factor. Cell. 1985 Jul;41(3):771–780. doi: 10.1016/s0092-8674(85)80058-1. [DOI] [PubMed] [Google Scholar]
  28. Kammerer W., Deuschle U., Gentz R., Bujard H. Functional dissection of Escherichia coli promoters: information in the transcribed region is involved in late steps of the overall process. EMBO J. 1986 Nov;5(11):2995–3000. doi: 10.1002/j.1460-2075.1986.tb04597.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Kingston R. E., Chamberlin M. J. Pausing and attenuation of in vitro transcription in the rrnB operon of E. coli. Cell. 1981 Dec;27(3 Pt 2):523–531. doi: 10.1016/0092-8674(81)90394-9. [DOI] [PubMed] [Google Scholar]
  30. 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]
  31. Kunkel T. A. Rapid and efficient site-specific mutagenesis without phenotypic selection. Proc Natl Acad Sci U S A. 1985 Jan;82(2):488–492. doi: 10.1073/pnas.82.2.488. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Lamond A. I., Travers A. A. Requirement for an upstream element for optimal transcription of a bacterial tRNA gene. Nature. 1983 Sep 15;305(5931):248–250. doi: 10.1038/305248a0. [DOI] [PubMed] [Google Scholar]
  33. Lawlor E. J., Baylis H. A., Chater K. F. Pleiotropic morphological and antibiotic deficiencies result from mutations in a gene encoding a tRNA-like product in Streptomyces coelicolor A3(2). Genes Dev. 1987 Dec;1(10):1305–1310. doi: 10.1101/gad.1.10.1305. [DOI] [PubMed] [Google Scholar]
  34. Leclerc G., Sirard C., Drapeau G. R. The Escherichia coli cell division mutation ftsM1 is in serU. J Bacteriol. 1989 Apr;171(4):2090–2095. doi: 10.1128/jb.171.4.2090-2095.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Lindsey D. F., Mullin D. A., Walker J. R. Characterization of the cryptic lambdoid prophage DLP12 of Escherichia coli and overlap of the DLP12 integrase gene with the tRNA gene argU. J Bacteriol. 1989 Nov;171(11):6197–6205. doi: 10.1128/jb.171.11.6197-6205.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Lupski J. R., Ruiz A. A., Godson G. N. Promotion, termination, and anti-termination in the rpsU-dnaG-rpoD macromolecular synthesis operon of E. coli K-12. Mol Gen Genet. 1984;195(3):391–401. doi: 10.1007/BF00341439. [DOI] [PubMed] [Google Scholar]
  37. Mizuno T. Random cloning of bent DNA segments from Escherichia coli chromosome and primary characterization of their structures. Nucleic Acids Res. 1987 Sep 11;15(17):6827–6841. doi: 10.1093/nar/15.17.6827. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. Mizushima-Sugano J., Kaziro Y. Regulation of the expression of the tufB operon: DNA sequences directly involved in the stringent control. EMBO J. 1985 Apr;4(4):1053–1058. doi: 10.1002/j.1460-2075.1985.tb03738.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Morgan E. A. Insertions of Tn 10 into an E. coli ribosomal RNA operon are incompletely polar. Cell. 1980 Aug;21(1):257–265. doi: 10.1016/0092-8674(80)90133-6. [DOI] [PubMed] [Google Scholar]
  40. Mulligan M. E., Brosius J., McClure W. R. Characterization in vitro of the effect of spacer length on the activity of Escherichia coli RNA polymerase at the TAC promoter. J Biol Chem. 1985 Mar 25;260(6):3529–3538. [PubMed] [Google Scholar]
  41. Mullin D. A., Garcia G. M., Walker J. R. An E. coli DNA fragment 118 base pairs in length provides dnaY+ complementing activity. Cell. 1984 Jun;37(2):669–674. doi: 10.1016/0092-8674(84)90399-4. [DOI] [PubMed] [Google Scholar]
  42. Munson L. M., Reznikoff W. S. Abortive initiation and long ribonucleic acid synthesis. Biochemistry. 1981 Apr 14;20(8):2081–2085. doi: 10.1021/bi00511a003. [DOI] [PubMed] [Google Scholar]
  43. Muramatsu S., Mizuno T. Nucleotide sequence of the region encompassing the int gene of a cryptic prophage and the dna Y gene flanked by a curved DNA sequence of Escherichia coli K12. Mol Gen Genet. 1990 Jan;220(2):325–328. doi: 10.1007/BF00260503. [DOI] [PubMed] [Google Scholar]
  44. Nachaliel N., Melnick J., Gafny R., Glaser G. Ribosome associated protein(s) specifically bind(s) to the upstream activator sequence of the E. coli rrnA P1 promoter. Nucleic Acids Res. 1989 Dec 11;17(23):9811–9822. doi: 10.1093/nar/17.23.9811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Nagase T., Ishii S., Imamoto F. Differential transcriptional control of the two tRNA(fMet) genes of Escherichia coli K-12. Gene. 1988 Jul 15;67(1):49–57. doi: 10.1016/0378-1119(88)90007-8. [DOI] [PubMed] [Google Scholar]
  46. Nakamura Y., Mizusawa S. In vivo evidence that the nusA and infB genes of E. coli are part of the same multi-gene operon which encodes at least four proteins. EMBO J. 1985 Feb;4(2):527–532. doi: 10.1002/j.1460-2075.1985.tb03660.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Nilsson L., Vanet A., Vijgenboom E., Bosch L. The role of FIS in trans activation of stable RNA operons of E. coli. EMBO J. 1990 Mar;9(3):727–734. doi: 10.1002/j.1460-2075.1990.tb08166.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Plaskon R. R., Wartell R. M. Sequence distributions associated with DNA curvature are found upstream of strong E. coli promoters. Nucleic Acids Res. 1987 Jan 26;15(2):785–796. doi: 10.1093/nar/15.2.785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Roesser J. R., Yanofsky C. Ribosome release modulates basal level expression of the trp operon of Escherichia coli. J Biol Chem. 1988 Oct 5;263(28):14251–14255. [PubMed] [Google Scholar]
  50. Ross W., Thompson J. F., Newlands J. T., Gourse R. L. E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo. EMBO J. 1990 Nov;9(11):3733–3742. doi: 10.1002/j.1460-2075.1990.tb07586.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
  52. Schmitz A., Galas D. J. The interaction of RNA polymerase and lac repressor with the lac control region. Nucleic Acids Res. 1979 Jan;6(1):111–137. doi: 10.1093/nar/6.1.111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Seed B., Sheen J. Y. A simple phase-extraction assay for chloramphenicol acyltransferase activity. Gene. 1988 Jul 30;67(2):271–277. doi: 10.1016/0378-1119(88)90403-9. [DOI] [PubMed] [Google Scholar]
  54. Sharp P. M., Li W. H. Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res. 1986 Oct 10;14(19):7737–7749. doi: 10.1093/nar/14.19.7737. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Siebenlist U., Simpson R. B., Gilbert W. E. coli RNA polymerase interacts homologously with two different promoters. Cell. 1980 Jun;20(2):269–281. doi: 10.1016/0092-8674(80)90613-3. [DOI] [PubMed] [Google Scholar]
  56. Spanjaard R. A., Chen K., Walker J. R., van Duin J. Frameshift suppression at tandem AGA and AGG codons by cloned tRNA genes: assigning a codon to argU tRNA and T4 tRNA(Arg). Nucleic Acids Res. 1990 Sep 11;18(17):5031–5036. doi: 10.1093/nar/18.17.5031. [DOI] [PMC free article] [PubMed] [Google Scholar]
  57. Stefano J. E., Gralla J. Lac UV5 transcription in vitro. Rate limitation subsequent to formation of an RNA polymerase-DNA complex. Biochemistry. 1979 Mar 20;18(6):1063–1067. doi: 10.1021/bi00573a020. [DOI] [PubMed] [Google Scholar]
  58. Tamura F., Nishimura S., Ohki M. The E. coli divE mutation, which differentially inhibits synthesis of certain proteins, is in tRNASer1. EMBO J. 1984 May;3(5):1103–1107. doi: 10.1002/j.1460-2075.1984.tb01936.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Thorbjarnardóttir S., Dingermann T., Rafnar T., Andrésson O. S., Söll D., Eggertsson G. Leucine tRNA family of Escherichia coli: nucleotide sequence of the supP(Am) suppressor gene. J Bacteriol. 1985 Jan;161(1):219–222. doi: 10.1128/jb.161.1.219-222.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  60. Travers A. A. Conserved features of coordinately regulated E. coli promoters. Nucleic Acids Res. 1984 Mar 26;12(6):2605–2618. doi: 10.1093/nar/12.6.2605. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Travers A. A., Lamond A. I., Weeks J. R. Alteration of the growth-rate-dependent regulation of Escherichia coli tyrT expression by promoter mutations. J Mol Biol. 1986 May 5;189(1):251–255. doi: 10.1016/0022-2836(86)90397-9. [DOI] [PubMed] [Google Scholar]
  62. Travers A. A. Promoter sequence for stringent control of bacterial ribonucleic acid synthesis. J Bacteriol. 1980 Feb;141(2):973–976. doi: 10.1128/jb.141.2.973-976.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  63. Vieira J., Messing J. The pUC plasmids, an M13mp7-derived system for insertion mutagenesis and sequencing with synthetic universal primers. Gene. 1982 Oct;19(3):259–268. doi: 10.1016/0378-1119(82)90015-4. [DOI] [PubMed] [Google Scholar]
  64. Wu H. M., Crothers D. M. The locus of sequence-directed and protein-induced DNA bending. Nature. 1984 Apr 5;308(5959):509–513. doi: 10.1038/308509a0. [DOI] [PubMed] [Google Scholar]
  65. Yeung T., Mullin D. A., Chen K. S., Craig E. A., Bardwell J. C., Walker J. R. Sequence and expression of the Escherichia coli recR locus. J Bacteriol. 1990 Oct;172(10):6042–6047. doi: 10.1128/jb.172.10.6042-6047.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  66. Zacharias M., Göringer H. U., Wagner R. Influence of the GCGC discriminator motif introduced into the ribosomal RNA P2- and tac promoter on growth-rate control and stringent sensitivity. EMBO J. 1989 Nov;8(11):3357–3363. doi: 10.1002/j.1460-2075.1989.tb08498.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  67. van Delft J. H., Mariñon B., Schmidt D. S., Bosch L. Transcription of the tRNA-tufB operon of Escherichia coli: activation, termination and antitermination. Nucleic Acids Res. 1987 Nov 25;15(22):9515–9530. doi: 10.1093/nar/15.22.9515. [DOI] [PMC free article] [PubMed] [Google Scholar]

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