Logo of embojLink to Publisher's site
EMBO J. 1987 Aug; 6(8): 2489–2492.
PMCID: PMC553658

Influence of the codon following the AUG initiation codon on the expression of a modified lacZ gene in Escherichia coli.

Abstract

In a lacZ expression vector (pMC1403Plac), all 64 codons were introduced immediately 3' from the AUG initiation codon. The expression of the second codon variants was measured by immunoprecipitation of the plasmid-coded fusion proteins. A 15-fold difference in expression was found among the codon variants. No distinct correlation could be made with the level of tRNA corresponding to the codons and large differences were observed between synonymous codons that use the same tRNA. Therefore the effect of the second codon is likely to be due to the influence of its composing nucleotides, presumably on the structure of the ribosomal binding site. An analysis of the known sequences of a large number of Escherichia coli genes shows that the use of codons in the second position deviates strongly from the overall codon usage in E. coli. It is proposed that codon selection at the second position is not based on requirements of the gene product (a protein) but is determined by factors governing gene regulation at the initiation step of translation.

Full text

Full text is available as a scanned copy of the original print version. Get a printable copy (PDF file) of the complete article (737K), or click on a page image below to browse page by page. Links to PubMed are also available for Selected References.

Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Busby S, Dreyfus M. Segment-specific mutagenesis of the regulatory region in the Escherichia coli galactose operon: isolation of mutations reducing the initiation of transcription and translation. Gene. 1983 Jan-Feb;21(1-2):121–131. [PubMed]
  • Chen EY, Seeburg PH. Supercoil sequencing: a fast and simple method for sequencing plasmid DNA. DNA. 1985 Apr;4(2):165–170. [PubMed]
  • Cone KC, Steege DA. Messenger RNA conformation and ribosome selection of translational reinitiation sites in the lac repressor mRNA. J Mol Biol. 1985 Dec 20;186(4):725–732. [PubMed]
  • Ganoza MC, Fraser AR, Neilson T. Nucleotides contiguous to AUG affect translational initiation. Biochemistry. 1978 Jul 11;17(14):2769–2775. [PubMed]
  • Gold L, Pribnow D, Schneider T, Shinedling S, Singer BS, Stormo G. Translational initiation in prokaryotes. Annu Rev Microbiol. 1981;35:365–403. [PubMed]
  • Gren EJ. Recognition of messenger RNA during translational initiation in Escherichia coli. Biochimie. 1984 Jan;66(1):1–29. [PubMed]
  • Grosjean H, Fiers W. Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene. 1982 Jun;18(3):199–209. [PubMed]
  • Gryczan TJ, Grandi G, Hahn J, Grandi R, Dubnau D. Conformational alteration of mRNA structure and the posttranscriptional regulation of erythromycin-induced drug resistance. Nucleic Acids Res. 1980 Dec 20;8(24):6081–6097. [PMC free article] [PubMed]
  • Gutell RR, Weiser B, Woese CR, Noller HF. Comparative anatomy of 16-S-like ribosomal RNA. Prog Nucleic Acid Res Mol Biol. 1985;32:155–216. [PubMed]
  • Hall MN, Gabay J, Débarbouillé M, Schwartz M. A role for mRNA secondary structure in the control of translation initiation. Nature. 1982 Feb 18;295(5850):616–618. [PubMed]
  • Horinouchi S, Weisblum B. Posttranscriptional modification of mRNA conformation: mechanism that regulates erythromycin-induced resistance. Proc Natl Acad Sci U S A. 1980 Dec;77(12):7079–7083. [PMC free article] [PubMed]
  • Hui A, Hayflick J, Dinkelspiel K, de Boer HA. Mutagenesis of the three bases preceding the start codon of the beta-galactosidase mRNA and its effect on translation in Escherichia coli. EMBO J. 1984 Mar;3(3):623–629. [PMC free article] [PubMed]
  • Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system. J Mol Biol. 1981 Sep 25;151(3):389–409. [PubMed]
  • Iserentant D, Fiers W. Secondary structure of mRNA and efficiency of translation initiation. Gene. 1980 Apr;9(1-2):1–12. [PubMed]
  • Kozak M. Comparison of initiation of protein synthesis in procaryotes, eucaryotes, and organelles. Microbiol Rev. 1983 Mar;47(1):1–45. [PMC free article] [PubMed]
  • Looman AC, de Gruyter M, Vogelaar A, van Knippenberg PH. Effects of heterologous ribosomal binding sites on the transcription and translation of the lacZ gene of Escherichia coli. Gene. 1985;37(1-3):145–154. [PubMed]
  • Looman AC, Bodlaender J, de Gruyter M, Vogelaar A, van Knippenberg PH. Secondary structure as primary determinant of the efficiency of ribosomal binding sites in Escherichia coli. Nucleic Acids Res. 1986 Jul 11;14(13):5481–5497. [PMC free article] [PubMed]
  • Matteucci MD, Heyneker HL. Targeted random mutagenesis: the use of ambiguously synthesized oligonucleotides to mutagenize sequences immediately 5' of an ATG initiation codon. Nucleic Acids Res. 1983 May 25;11(10):3113–3121. [PMC free article] [PubMed]
  • Movva NR, Nakamura K, Inouye M. Amino acid sequence of the signal peptide of ompA protein, a major outer membrane protein of Escherichia coli. J Biol Chem. 1980 Jan 10;255(1):27–29. [PubMed]
  • Munson LM, Stormo GD, Niece RL, Reznikoff WS. lacZ translation initiation mutations. J Mol Biol. 1984 Aug 25;177(4):663–683. [PubMed]
  • Schottel JL, Sninsky JJ, Cohen SN. Effects of alterations in the translation control region on bacterial gene expression: use of cat gene constructs transcribed from the lac promoter as a model system. Gene. 1984 May;28(2):177–193. [PubMed]
  • Scherer GF, Walkinshaw MD, Arnott S, Morré DJ. The ribosome binding sites recognized by E. coli ribosomes have regions with signal character in both the leader and protein coding segments. Nucleic Acids Res. 1980 Sep 11;8(17):3895–3907. [PMC free article] [PubMed]
  • Stormo GD, Schneider TD, Gold LM. Characterization of translational initiation sites in E. coli. Nucleic Acids Res. 1982 May 11;10(9):2971–2996. [PMC free article] [PubMed]
  • Stormo GD, Schneider TD, Gold L. Quantitative analysis of the relationship between nucleotide sequence and functional activity. Nucleic Acids Res. 1986 Aug 26;14(16):6661–6679. [PMC free article] [PubMed]
  • Taniguchi T, Weissmann C. Inhibition of Qbeta RNA 70S ribosome initiation complex formation by an oligonucleotide complementary to the 3' terminal region of E. coli 16S ribosomal RNA. Nature. 1978 Oct 26;275(5682):770–772. [PubMed]
  • Varenne S, Buc J, Lloubes R, Lazdunski C. Translation is a non-uniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains. J Mol Biol. 1984 Dec 15;180(3):549–576. [PubMed]
  • Wood CR, Boss MA, Patel TP, Emtage JS. The influence of messenger RNA secondary structure on expression of an immunoglobulin heavy chain in Escherichia coli. Nucleic Acids Res. 1984 May 11;12(9):3937–3950. [PMC free article] [PubMed]
  • Yanofsky C. Attenuation in the control of expression of bacterial operons. Nature. 1981 Feb 26;289(5800):751–758. [PubMed]
  • Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981 Jan 10;9(1):133–148. [PMC free article] [PubMed]
  • Berkhout B, van Duin J. Mechanism of translational coupling between coat protein and replicase genes of RNA bacteriophage MS2. Nucleic Acids Res. 1985 Oct 11;13(19):6955–6967. [PMC free article] [PubMed]
  • Buell G, Schulz MF, Selzer G, Chollet A, Movva NR, Semon D, Escanez S, Kawashima E. Optimizing the expression in E. coli of a synthetic gene encoding somatomedin-C (IGF-I). Nucleic Acids Res. 1985 Mar 25;13(6):1923–1938. [PMC free article] [PubMed]

Articles from The EMBO Journal are provided here courtesy of The European Molecular Biology Organization

Formats:

Related citations in PubMed

Cited by other articles in PMC

See all...

Links

Recent Activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...