Skip to main content
SpringerLink
Log in
Book cover

Regulation of Gene Expression in Escherichia coli pp 47–65Cite as

Codon Context, Translational Step-Times and Attenuation

  • Chapter

  • 294 Accesses

Abstract

Charles Yanofsky and his co-workers have provided us with a detailed understanding of the attenuation mechanism for the regulation of the tryptophan operon of Escherichia coli. This understanding is based on the results of rigorous experimental documentation gathered over the course of the last 15 years. During this time, attenuation mechanisms have also been elucidated for several other operons required for the biosynthesis of amino acids and intermediary metabolites in bacteria. Most recently, Yanofsky and his co-workers have described a model for setting the basal level of transcriptional readthrough at the attenuator of the trp operon. This model, which is supported by a great deal of experimental evidence and has been reviewed elsewhere,1–3 emphasizes the importance of the timing and synchronization of the movement of an RNA polymerase and a ribosome through the leader-attenuator region, i.e., the mechanistic importance of the relative transcription and translation elongation rates for attenuation. While much has been learned about the transit of an RNA polymerase molecule through the leader-attenuator region of the trp operon, little is known about the mechanisms that influence the movement of the ribosome. Indeed, little is known about the mechanisms that influence elongation rates and pausing during the translation of any messenger RNA.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Landick R, Yanofsky C. Transcription attenuation. In: Neidheidhardt FC, Ingraham JL, Low KB, Magasanik B, Schaechter M, Umbarger HE, eds. Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. Washington, D.C.: American Society for Microbiology, 1987:1276–1301.

    Google Scholar 

  2. Landick R, Turnbough CL. Transcriptional attenuation. In: McKnight SL, Yamamoto K, ed. Transcriptional Regulation. Cold Spring Harbor, NY: Cold Spring Harbor Press, 1992:407–446.

    Google Scholar 

  3. Hatfield GW. A two ribosome model for attenuation. In: Ilan J, ed. Translational expression of gene expression 2. New York, NY: Plenum Publishing Corporation, 1993:1–22.

    Chapter  Google Scholar 

  4. Hatfield GW, Gutman GA. Codon pair utilization bias in bacteria, yeast and mammals. In: Hatfield DL, Lee BJ, Pirtle RM, ed. Transfer RNA in Protein Synthesis. Boca Raton, LA: CRC Press, 1993:157–189.

    Google Scholar 

  5. Gutman GA, Hatfield GW. Nonrandom utilization of codon pairs in Escherichia coli. Proc Natl Acad Sci USA 1989; 86(10):3699–703.

    Article  Google Scholar 

  6. Aloni Y, Hay N. Attenuation may regulate gene expression in animal viruses and cells. CRC Crit Rev Biochem 1985; 18(4):327–83.

    Article  Google Scholar 

  7. Yanofsky C. Transcription attenuation. J Biol Chem 1988; 263(2):609–12.

    Google Scholar 

  8. Bertrand K, Korn LJ, Lee F, Yanofsky C. The attenuator of the tryptophan Operon of Escherichia coli. Heterogeneous 3′-OH termini in vivo and deletion mapping of functions. J Mol Biol 1977; 117(1):227–47.

    Article  Google Scholar 

  9. Bertrand K, Squires C, Yanofsky C. Transcription termination in vivo in the leader region of the tryptophan Operon of Escherichia coli. J Mol Biol 1976; 103(2):319–37.

    Article  Google Scholar 

  10. Bertrand K, Yanofsky C. Regulation of transcription termination in the leader region of the tryptophan Operon of Escherichia coli involves tryptophan or its metabolic product. J Mol Biol 1976; 103(2):339–49.

    Article  Google Scholar 

  11. Lee F, Squires CL, Squires C, Yanofsky C. Termination of transcription in vitro in the Escherichia coli tryptophan Operon leader region. J Mol Biol 1976; 103(2):383–93.

    Article  Google Scholar 

  12. Friden P, Newman T, Freundlich M. Nucleotide sequence of the ilvB promoter-regulatory region: a biosynthetic operon controlled by attenuation and cyclic AMP. Proc Natl Acad Sci USA 1982; 79(20):6156–60.

    Article  Google Scholar 

  13. Hauser CA, Hatfield GW. Nucleotide sequence of the ilvB multivalent attenuator region of Escherichia coli K12. Nucleic Acids Res 1983; ll(l):127–39.

    Article  Google Scholar 

  14. Lawther RP, Hatfield GW. Multivalent translational control of transcription termination at attenuator of ilvGEDA operon of Escherichia coli K-12. Proc Natl Acad Sci USA 1980; 77(4): 1862–6.

    Article  Google Scholar 

  15. Nargang FE, Subrahmanyam CS, Umbarger HE. Nucleotide sequence of ilvGEDA operon attenuator region of Escherichia coli. Proc Natl Acad Sci USA 1980; 77(4):1823–7.

    Article  Google Scholar 

  16. Gardner JF. Regulation of the threonine operon: tandem threonine and isoleucine codons in the control region and translational control of transcription termination. Proc Natl Acad Sci USA 1979; 76(4): 1706–10.

    Article  Google Scholar 

  17. Gemmill RM, Sessler SR, Calvo JM. leu operon of Salmonnella typhimurium is controlled by attenuation. Proc Natl Acad Sci USA 1979; 76:4941–4945.

    Article  Google Scholar 

  18. Barnes WM. DNA sequence from the histidine control region: seven histidine codons in a row. Proc Natl Acad Sci USA 1978; 75(4281–4285).

    Article  Google Scholar 

  19. DiNocera PP, Blasi F, DiLauro R, Frunzio R, Bruni CB. Nucleotide sequence of the attenuator region of the histidine operon of Escherichia coli K-12. Proc Natl Acad Sci USA 1978; 75:4276–4280.

    Article  Google Scholar 

  20. Zurawski G, Brown K, Killingly D, Yanofsky C. Nucleotide sequence of the leader region of the phenylalanine operon of Escherichia coli. Proc Natl Acad Sci USA 1978; 75(9):4271–5.

    Article  Google Scholar 

  21. Curran JF, Yarus M. Use of tRNA suppressors to probe regulation of Escherichia coli release factor 2. J Mol Biol 1988; 203(1):75–83.

    Article  Google Scholar 

  22. Gausing K. Efficiency of protein and messenger RNA synthesis in bacteriophage T4-infected cells of Escherichia coli. J Mol Biol 1972; 71(3):529–45.

    Article  Google Scholar 

  23. Roesser JR, Nakamura Y, Yanofsky C. Regulation of basal level expression of the tryptophan operon of Escherichia coli. J Biol Chem 1989; 264(21):12284–8.

    Google Scholar 

  24. Roesser JR, Yanofsky C. Ribosome release modulates basal level expression of the trp operon of Escherichia coli. J Biol Chem 1988; 263(28): 14251–5.

    Google Scholar 

  25. Caskey CT. Peptide chain termination. Trends Biochem Sci 1980; 54:234–237.

    Article  Google Scholar 

  26. Suzuki H, Kunisawa T, Otsuka J. Theoretical evaluation of transcriptional pausing effect on the attenuation of trp leader sequence. Biophys J 1986; 49:425–436.

    Article  Google Scholar 

  27. Steitz JA. RNA-RNA interactions in ribosome translation initiation. In: Chambliss G, Craven GR, Davies J, Davis K, Kahan L, Nomura M, eds. Ribosomes: Structure Function and Genetics. Baltimore: University Park Press, 1980:479–495.

    Google Scholar 

  28. Protzel A, Morris AJ. Gel chromatographic analysis of nascent globin chains. Evidence of nonuniform size distribution. J Biol Chem 1974; 249:4594.

    Google Scholar 

  29. Lizardi PM, Mahdari V, Shields D, Candelas G. Discontinuous translation of silk fibroin in a reticulocyte cell-free system and in intact silk gland cells. Proc Natl Acad Sci USA 1979; 76:6211.

    Article  Google Scholar 

  30. Candelas G, Candelas T, Ortiz A, Rodriguez O. Translational pauses during a spider fibroin synthesis. Biochem Biophys Res Commun 1983; 116:1033.

    Article  Google Scholar 

  31. Varenne S, Knibiehler M, Cavard D, Morion J, Lazdunski C. Variable rate of polypeptide elongation for colicins A, E2, and E3. J Mol Biol 1982; 159:57.

    Article  Google Scholar 

  32. Chaney W, Morris A. Nonuniform size distribution of nascent peptides. The effect of messenger RNA structure upon the rate of translation. Arch Biochem Biophys 1979; 194:283.

    Article  Google Scholar 

  33. Randall LL, Josefsson LG, Hardy SJS. Novel intermediates in the synthesis of maltose-binding protein in Escherichia coli. Eur J Biochem 1980; 107:375.

    Article  Google Scholar 

  34. Abraham AK, Pihl A. Variable rate of polypeptide chain elongation in vitro. Eur J Biochem 1980; 106:257.

    Article  Google Scholar 

  35. Wolin SL, Walter P. Ribosome pausing and stacking during translation of a eukaryotic mRNA. Embo J 1988; 7(11):3559–69.

    Google Scholar 

  36. Gouy M, Gautier C. Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res 1982; 10:7055–61.

    Article  Google Scholar 

  37. Liljenstrom H, von Heinje G. Translation rate modification by preferential codon usage. J Theor Biol 1987; 124:43–8.

    Article  Google Scholar 

  38. Kuroda MI, Yanofsky C. Evidence for the transcript secondary structures predicted to regulate transcription attenuation in the trp Operon. J Biol Chem 1984; 259(20):12838–43.

    Google Scholar 

  39. Oxender DL, Zurawski G, Yanofsky C. Attenuation in the Escherichia coli tryptophan Operon: role of RNA secondary structure involving the tryptophan codon region. Proc Natl Acad Sci USA 1979; 76(11):5524–8.

    Article  Google Scholar 

  40. Kolter R, Yanofsky C. Genetic analysis of the tryptophan operon regulatory region using site-directed mutagenesis. J Mol Biol 1984; 175(3): 299–312.

    Article  Google Scholar 

  41. Landick R, Yanofsky C, Choo K, Phung L. Replacement of the Escherichia coli trp operon attenuation control codons alters operon expression. J Mol Biol 1990; 216(1):25–37.

    Article  Google Scholar 

  42. Bonekamp F, Dalbege H, Christensen T, Jensen KF. Translation rates of individual codons are not correlated with tRNA abundances or with frequencies of utilization in Escherichia coli. J Bact 1989; 171(11):5812–5816.

    Google Scholar 

  43. Robinson M, Lilley R, Little S et al. Codon usage can affect efficiency of translation of genes in Escherichia coli. Nucleic Acids Res 1984; 12:6663.

    Article  Google Scholar 

  44. . Lynn SP, Burton WS, Donohue TJ, Gould RM, Gumport RI, Gardner JF. 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; 194(l):59–69.

    Article  Google Scholar 

  45. Chen JW, Bennett DC, Umbarger HE. Specificity of attenuation control in the ilvGMEDA operon of Escherichia coli K-12 [published erratum appears in J Bacteriol 1991 May; 173(10):3269]. J Bacteriol 1991; 173(7):2328–40.

    Google Scholar 

  46. . Chen JW, Harms E, Umbarger HE. Mutations replacing the leucine codons or altering the length of the amino acid-coding portion of the ilvGMEDA leader region of Escherichia coli. J Bacteriol 1991; 173(7): 2341–53.

    Google Scholar 

  47. . Carter PW, Weiss DL, Weith HL, Calvo JM. Mutations that convert the four leucine codons of the Salmonella typhimurium leu leader to four threonine codons. J Bacteriol 1985; 162(3):943–9.

    Google Scholar 

  48. Irwin B, Heck JD, Hatfield GW. Codon pair utilization biases influence translational elongation step times. J Biol Chem 1995; 270(39):22801–6.

    Article  Google Scholar 

Download references

Authors
  1. G. W. Hatfield
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

Copyright information

© 1996 R.G. Landes Company

About this chapter

Cite this chapter

Hatfield, G.W. (1996). Codon Context, Translational Step-Times and Attenuation. In: Regulation of Gene Expression in Escherichia coli . Springer, Boston, MA. https://doi.org/10.1007/978-1-4684-8601-8_4

Download citation

  • DOI: https://doi.org/10.1007/978-1-4684-8601-8_4

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4684-8603-2

  • Online ISBN: 978-1-4684-8601-8

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics

Search

Navigation