Skip to main content
PMC home page
Journal of Bacteriology logoLink to Journal of Bacteriology
. 1987 Dec;169(12):5668–5677. doi: 10.1128/jb.169.12.5668-5677.1987

Role of codon choice in the leader region of the ilvGMEDA operon of Serratia marcescens.

E Harms 1, H E Umbarger 1
PMCID: PMC214033  PMID: 2824442

Abstract

Leucine participates in multivalent repression of the Serratia marcescens ilvGMEDA operon by attenuation (J.-H. Hsu, E. Harms, and H.E. Umbarger, J. Bacteriol. 164:217-222, 1985), although there is only one single leucine codon that could be involved in this type of control. This leucine codon is the rarely used CUA. The contribution of this leucine codon to the control of transcription by attenuation was examined by replacing it with the commonly used leucine codon CUG and with a nonregulatory proline codon, CCG. These changes left intact the proposed secondary structure of the leader. The effects of the codon changes were assessed by placing the mutant leader regions upstream of the ilvGME structural genes or the cat gene and measuring acetohydroxy acid synthase II, transaminase B, or chloramphenicol acetyltransferase activities in cells grown under limiting and repressing conditions. The presence of the common leucine codon in place of the rare leucine codon reduced derepression by about 70%. Eliminating the leucine codon by converting it to proline abolished leucine control. Furthermore, a possible context effect of the adjacent upstream serine codon on leucine control was examined by changing it into a glycine codon.

Full text

PDF
5668

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Bennett D. C., Umbarger H. E. Isolation and analysis of two Escherichia coli K-12 ilv attenuator deletion mutants with high-level constitutive expression of an ilv-lac fusion operon. J Bacteriol. 1984 Mar;157(3):839–845. doi: 10.1128/jb.157.3.839-845.1984. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. 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]
  3. 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]
  4. Carter P. W., Bartkus J. M., Calvo J. M. Transcription attenuation in Salmonella typhimurium: the significance of rare leucine codons in the leu leader. Proc Natl Acad Sci U S A. 1986 Nov;83(21):8127–8131. doi: 10.1073/pnas.83.21.8127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Friedberg D., Mikulka T. W., Jones J., Calvo J. M. flrB, a regulatory locus controlling branched-chain amino acid biosynthesis in Salmonella typhimurium. J Bacteriol. 1974 Jun;118(3):942–951. doi: 10.1128/jb.118.3.942-951.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Gayda D. J., Leathers T. D., Noti J. D., Smith F. J., Smith J. M., Subrahmanyam C. S., Umbarger H. E. Location of the multivalent control site for the ilvEDA operon of Escherichia coli. J Bacteriol. 1980 May;142(2):556–567. doi: 10.1128/jb.142.2.556-567.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Gemmill R. M., Wessler S. R., Keller E. B., Calvo J. M. leu operon of Salmonella typhimurium is controlled by an attenuation mechanism. Proc Natl Acad Sci U S A. 1979 Oct;76(10):4941–4945. doi: 10.1073/pnas.76.10.4941. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Gorman C. M., Moffat L. F., Howard B. H. Recombinant genomes which express chloramphenicol acetyltransferase in mammalian cells. Mol Cell Biol. 1982 Sep;2(9):1044–1051. doi: 10.1128/mcb.2.9.1044. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Greener A., Hill C. W. Identification of a novel genetic element in Escherichia coli K-12. J Bacteriol. 1980 Oct;144(1):312–321. doi: 10.1128/jb.144.1.312-321.1980. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Harms E., Hsu J. H., Subrahmanyam C. S., Umbarger H. E. Comparison of the regulatory regions of ilvGEDA operons from several enteric organisms. J Bacteriol. 1985 Oct;164(1):207–216. doi: 10.1128/jb.164.1.207-216.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hauser C. A., Hatfield G. W. Attenuation of the ilvB operon by amino acids reflecting substrates or products of the ilvB gene product. Proc Natl Acad Sci U S A. 1984 Jan;81(1):76–79. doi: 10.1073/pnas.81.1.76. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Hauser C. A., Sharp J. A., Hatfield L. K., Hatfield G. W. Pausing of RNA polymerase during in vitro transcription through the ilvB and ilvGEDA attenuator regions of Escherichia coli K12. J Biol Chem. 1985 Feb 10;260(3):1765–1770. [PubMed] [Google Scholar]
  13. Hsu J. H., Harms E., Umbarger H. E. Leucine regulation of the ilvGEDA operon of Serratia marcescens by attenuation is modulated by a single leucine codon. J Bacteriol. 1985 Oct;164(1):217–222. doi: 10.1128/jb.164.1.217-222.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Ikemura T. Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J Mol Biol. 1982 Jul 15;158(4):573–597. doi: 10.1016/0022-2836(82)90250-9. [DOI] [PubMed] [Google Scholar]
  15. Johnson D. I., Somerville R. L. Evidence that repression mechanisms can exert control over the thr, leu, and ilv operons of Escherichia coli K-12. J Bacteriol. 1983 Jul;155(1):49–55. doi: 10.1128/jb.155.1.49-55.1983. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kisumi M., Komatsubara S., Chibata I. Multivalent repression and genetic depression of isoleucine-valine biosynthetic enzymes in Serratia marcescens. J Bacteriol. 1971 Sep;107(3):824–827. doi: 10.1128/jb.107.3.824-827.1971. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Kline E. L. New amino acid regulatory locus having unusual properties in heterozygous merodiploids. J Bacteriol. 1972 Jun;110(3):1127–1134. doi: 10.1128/jb.110.3.1127-1134.1972. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Kolter R., Yanofsky C. Attenuation in amino acid biosynthetic operons. Annu Rev Genet. 1982;16:113–134. doi: 10.1146/annurev.ge.16.120182.000553. [DOI] [PubMed] [Google Scholar]
  19. Lawther R. P., Calhoun D. H., Adams C. W., Hauser C. A., Gray J., Hatfield G. W. Molecular basis of valine resistance in Escherichia coli K-12. Proc Natl Acad Sci U S A. 1981 Feb;78(2):922–925. doi: 10.1073/pnas.78.2.922. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Lawther R. P., Hatfield G. W. Multivalent translational control of transcription termination at attenuator of ilvGEDA operon of Escherichia coli K-12. Proc Natl Acad Sci U S A. 1980 Apr;77(4):1862–1866. doi: 10.1073/pnas.77.4.1862. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Lederberg E. M., Cohen S. N. Transformation of Salmonella typhimurium by plasmid deoxyribonucleic acid. J Bacteriol. 1974 Sep;119(3):1072–1074. doi: 10.1128/jb.119.3.1072-1074.1974. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Lynn S. P., Burton W. S., Donohue T. J., Gould R. M., Gumport R. I., Gardner J. F. Specificity of the attenuation response of the threonine operon of Escherichia coli is determined by the threonine and isoleucine codons in the leader transcript. J Mol Biol. 1987 Mar 5;194(1):59–69. doi: 10.1016/0022-2836(87)90715-7. [DOI] [PubMed] [Google Scholar]
  23. Nargang F. E., Subrahmanyam C. S., Umbarger H. E. Nucleotide sequence of ilvGEDA operon attenuator region of Escherichia coli. Proc Natl Acad Sci U S A. 1980 Apr;77(4):1823–1827. doi: 10.1073/pnas.77.4.1823. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Novick R. P., Clowes R. C., Cohen S. N., Curtiss R., 3rd, Datta N., Falkow S. Uniform nomenclature for bacterial plasmids: a proposal. Bacteriol Rev. 1976 Mar;40(1):168–189. doi: 10.1128/br.40.1.168-189.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Prentki P., Krisch H. M. In vitro insertional mutagenesis with a selectable DNA fragment. Gene. 1984 Sep;29(3):303–313. doi: 10.1016/0378-1119(84)90059-3. [DOI] [PubMed] [Google Scholar]
  26. Rahmanian M., Claus D. R., Oxender D. L. Multiplicity of leucine transport systems in Escherichia coli K-12. J Bacteriol. 1973 Dec;116(3):1258–1266. doi: 10.1128/jb.116.3.1258-1266.1973. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. 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]
  28. Sidikaro J., Masayasu N. In vitro synthesis of the E3 immunity protein directed by Col E3 plasmid deoxyribonucleic acid. J Biol Chem. 1975 Feb 10;250(3):1123–1131. [PubMed] [Google Scholar]
  29. Smith J. M., Smith F. J., Umbarger H. E. Mutations affecting the formation of acetohydroxy acid synthase II in Escherichia coli K-12. Mol Gen Genet. 1979 Feb 1;169(3):299–314. doi: 10.1007/BF00382276. [DOI] [PubMed] [Google Scholar]
  30. Southern E. M. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J Mol Biol. 1975 Nov 5;98(3):503–517. doi: 10.1016/s0022-2836(75)80083-0. [DOI] [PubMed] [Google Scholar]
  31. Sprinzl M., Grueter F., Spelzhaus A., Gauss D. H. Compilation of tRNA sequences. Nucleic Acids Res. 1980 Jan 11;8(1):r1–r22. [PMC free article] [PubMed] [Google Scholar]
  32. Stroynowski I., Yanofsky C. Transcript secondary structures regulate transcription termination at the attenuator of S. marcescens tryptophan operon. Nature. 1982 Jul 1;298(5869):34–38. doi: 10.1038/298034a0. [DOI] [PubMed] [Google Scholar]
  33. Tsui P., Freundlich M. Starvation for ilvB operon leader amino acids other than leucine or valine does not increase acetohydroxy acid synthase activity in Escherichia coli. J Bacteriol. 1985 Jun;162(3):1314–1316. doi: 10.1128/jb.162.3.1314-1316.1985. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. 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]
  35. Yanisch-Perron C., Vieira J., Messing J. Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene. 1985;33(1):103–119. doi: 10.1016/0378-1119(85)90120-9. [DOI] [PubMed] [Google Scholar]
  36. Zoller M. J., Smith M. Oligonucleotide-directed mutagenesis of DNA fragments cloned into M13 vectors. Methods Enzymol. 1983;100:468–500. doi: 10.1016/0076-6879(83)00074-9. [DOI] [PubMed] [Google Scholar]

Articles from Journal of Bacteriology are provided here courtesy of American Society for Microbiology (ASM)

RESOURCES