Skip to main content
SpringerLink
Log in

The rates of macromolecular chain elongation modulate the initiation frequencies for transcription and translation inEscherichia coli

  • Into The Black Box
  • Published:
Antonie van Leeuwenhoek Aims and scope Submit manuscript

Abstract

Here we show that most macromolecular biosynthesis reactions in growing bacteria are sub-saturated with substrate. The experiments should in part test predictions from a previously proposed model (Jensen & Pedersen 1990) which proposed a central role for the rates of the RNA and peptide chain elongation reactions in determining the concentration of initiation competent RNA polymerases and ribosomes and thereby the initiation frequencies for these reactions. We have shown that synthesis of ribosomal RNA and the concentration of ppGpp did not exhibit the normal inverse correlation under balanced growth conditions in batch cultures when the RNA chain elongation rate was limited by substrate supply. The RNA chain elongation rate for the polymerase transcribinglacZ mRNA was directly measured and found to be reduced by two-fold under conditions of high ppGpp levels.

In the case of translation, we have shown that the peptide elongation rate varied at different types of codons and even among codons read by the same tRNA species. The faster translated codons probably have the highest cognate tRNA concentration and the highest affinity to the tRNA. Thus, the ribosome may operate close to saturation at some codons and be unsaturated at synonymous codons. Therefore, not only translation of the codons for the seven amino acids, whose biosynthesis is regulated by attenuation, but also a substantial fraction of the other translation reactions may be unsaturated.

Recently, we have obtained results which indicate that also many ribosome binding sites are unsaturated with their substrate, i.e. with ribosomes. This observation affects the interpretation of many results obtained by use of reporter genes, because the expression from such genes is strongly influenced by the general physiology of the cell.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Baracchini E & Bremer H (1988) Stringent and growth control of rRNA synthesis inEscherichia coli are both mediated by ppGpp. J. Biol. Chem. 263: 2597–2602

    PubMed  Google Scholar 

  • Bergmann JE & Lodish H (1979) A kinetic model of protein synthesis. Proc. Natl. Acad. Sci. USA 254: 11927–11937

    Google Scholar 

  • Bonekamp F, Dalbøge H, Christensen T & Jensen KF (1989) Translation rates of individual codons are not correlated with tRNA abundance or with frequencies of utilization inEscherichia coli. J. Bacteriol. 171: 5812–5816

    PubMed  Google Scholar 

  • Bremer H & Dennis PP (1987) Modulation of chemical composition and other parameters of the cell by growth-rate. In: Neidhardt FC, Ingraham JC, Low KB, Magasanik B, Schaecter M & Umbarger HE (Eds)Escherichia coli andSalmonella typhimurium. Cellular and Molecular Biology (pp 1527–1542). American Society for Microbiology, Washington DC

    Google Scholar 

  • Bulmer M (1988) Codon usage and intragenic position. J. Theor. Biol. 133: 67–71

    PubMed  Google Scholar 

  • Cashel M & Gallant J (1969) Two compounds implicated in the function of the RC gene ofEscherichia coli. Nature (London) 221: 838–841

    PubMed  Google Scholar 

  • Cashel M & Rudd KE (1987) The stringent response. In: Neidhardt FC, Ingraham JC, Low KB, Magasanik B, Schaecter M & Umbarger HE (Eds)Escherichia coli andSalmonella typhimurium. Cellular and Molecular Biology (pp 1410–1438). American Society for Microbiology, Washington DC

    Google Scholar 

  • Clark B & Maaløe O (1967) DNA and the division cycle inEscherichia coli. J. Molec. Biol. 23: 99–112

    Google Scholar 

  • Dennis PP & Nomura M (1974) Stringent control of ribosomal protein gene expression inEscherichia coli. Proc. Nat. Acad. Sci. USA 71: 3819–3823

    PubMed  Google Scholar 

  • Dickson RR, Gaal T, de Boer HA, de Haseth PL & Gourse RL (1989) Identification of promoter mutants defective in growth-rate-dependent regulation of rRNA transcription inEscherichia coli. J. Bacteriol. 171: 4862–4870

    PubMed  Google Scholar 

  • Dix DB & Thompson RC (1986) Elongation factor Tu-guanosine 3′-diphosphate 5′-diphosphate complex increases the fidelity of proof reading in protein synthesis: mechanism for reducing translational errors introduced by amino acid starvation. Proc. Natl. Acad. Sci. USA 83: 2027–2031

    PubMed  Google Scholar 

  • Emilsson V & Kurland CG (1990) Growth rate dependence of transfer RNA abundance inEscherichia coli. EMBO J. 9: 4359–4366

    PubMed  Google Scholar 

  • Gaal T, Barkel J, Dickson RR, de Boer HA, de Haseth PL, Alavi H & Gourse RL (1989) Saturation mutagenesis of anEscherichia coli rRNA promoter and initial characterization of promoter variants. J. Bacteriol. 171: 4852–4861

    PubMed  Google Scholar 

  • Gaal T & Gourse RL (1990) Guanosine 3′ diphosphate 5′ diphosphate is not required for growth rate dependent control of rRNA synthesis inE. coli. Proc. Natl. Acad. Sci. USA 87: 5533–5537

    PubMed  Google Scholar 

  • Gallant J, Irr J & Cashel M (1971) The mechanism of amino acid control of guanylate and adenylate synthesis. J. Biol. Chem. 246: 5812–5816

    PubMed  Google Scholar 

  • Gallant J, Weiss R, Murphy J & Brown M (1984) Some puzzles of translational accuracy. In: Schaechter M, Neidhardt FC, Ingraham JL & Kjeldgaard NO (Eds) The Molecular Biology of Bacterial Growth (pp 92–107). Jones & Bartlett, Boston, USA

    Google Scholar 

  • Hall B & Gallant J (1972) Defective translation in RC-cells. Nature (London). New Biol. 237: 131–135

    Google Scholar 

  • Hansen MT, Pato ML, Molin S, Fiil NP & von Meyenburg K (1975). Simple downshift and resulting lack of correlation between ppGpp pool size and ribonucleic acid accumulation. J. Bacteriol. 122: 585–591

    PubMed  Google Scholar 

  • Haseltine WA & Block R (1973) Synthesis of guanosine tetra- and pentaphosphate requires the presence of a codon-specific, uncharged transfer ribonucleic acid in the acceptor site of ribosomes. Proc. Natl. Acad. Sci. USA 70: 1564–1568

    PubMed  Google Scholar 

  • Ingraham JL, Maaløe O & Neidhardt FC (1983) Growth of the Bacterial Cell. Sinauer Associates, Inc., Sunderland, Mass., USA

    Google Scholar 

  • Jensen KF. & Pedersen S (1990) Metabolic growth rate control inEscherichia coli may be a consequence of subsaturation of the macromolecular biosynthetic apparatus with substrates and catalytic components. Microbiol. Rev. 54: 89–100

    PubMed  Google Scholar 

  • Johnsen K, Molin S, Karlström O & Maaløe O (1977) Control of protein synthesis inEscherichia coli. Analysis of an energy source shift-down. J. Bacteriol. 131: 18–29

    PubMed  Google Scholar 

  • Kato M, Nishikawa M, Uritani M, Miyazaki M & Takemura S (1990) The difference in the type of codon-anticodon base pairing at the ribosomal P-site is one of the determinants of the translation rate. J. Biochem. 107: 242–247

    PubMed  Google Scholar 

  • Kingston RE, Nierman WC & Chamberlin MJ (1981) A direct effect of guanosine tetraphosphate on pausing ofEscherichia coli RNA polymerase during RNA chain elongation. J. Biol. Chem. 256: 2787–2797

    PubMed  Google Scholar 

  • Komine Y, Adachi T, Inokuchi H & Ozeki H (1990) Genomic organization and physical mapping of the transfer RNA genes inEscherichia coli K12. J. Mol. Biol. 212: 579–598

    PubMed  Google Scholar 

  • Kurland CG (1987) Strategies for efficiency and accuracy in gene expression. I. The major codon preference: a growth optimization strategy. Trends Biochem. Sci. 12: 126–128

    Google Scholar 

  • Landick R & Yanofsky C (1987) Transcription attenuation. In: Neidhardt FC, Ingraham JC, Low KB, Magasanik B, Schaecter M & Umbarger HE (Eds)Escherichia coli andSalmonella typhimurium. Cellular and Molecular Biology (pp 1276–1301). American Society for Microbiology, Washington DC

    Google Scholar 

  • Lazzarini RA, Cashel M & Gallant J (1971) On the regulation of guanosine tetraphosphate levels in stringent and relaxed strains ofEscherichia coli. J. Biol. Chem. 246: 4381–4385

    PubMed  Google Scholar 

  • Leavitt RI & Umbarger HE (1962) Isoleucine and valine metabolism inEscherichia coli XI: Valine inhibition of the growth ofEscherichia coli strain K12. J. Bacteriol. 83: 624–630

    PubMed  Google Scholar 

  • Miller J (1972) Experiments in Molecular Genetics, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, USA

    Google Scholar 

  • Nunn W & Cronan J (1974) rel gene control of lipid synthesis inEscherichia coli. Evidence for eliminating fatty acid synthesis as the sole regulatory site. J. Biol. Chem. 249: 3994–3996

    PubMed  Google Scholar 

  • O'Farrell PH (1978) The suppression of defective translation by ppGpp and its role in the stringent response. Cell 14: 545–557

    PubMed  Google Scholar 

  • Olins PO & Rangwala SH (1989) A novel sequence element derived from bacteriophage T7 mRNA acts as an enhancer of translation of thelacZ gene in Escherichia coli. J. Biol. Chem. 264: 16973–16976

    PubMed  Google Scholar 

  • Pedersen FS, Lund E & Kjeldgaard NO (1973) Codon specific tRNA dependentin vitro synthesis of ppGpp and pppGpp. Nature (London) New Biol. 243: 13–15

    Google Scholar 

  • Pedersen S (1984).Escherichia coli ribosomes translatein vivo with variable rate. EMBO J. 3: 2895–2898

    PubMed  Google Scholar 

  • Poulsen P & Jensen KF (1987) Effect of UTP and GTP pools on attenuation at thepyrE gene ofEscherichia coli. Mol. Gen. Genet. 208: 152–158

    PubMed  Google Scholar 

  • Reeh S, Pedersen S & Friesen JD (1976) Biosynthetic regulation of individual proteins inrelA + andrelA strains ofEscherichia coli during amino acid starvation. Mol. Gen. Genet. 149: 279–289

    PubMed  Google Scholar 

  • Sørensen MA, Kurland CG & Pedersen S (1989) Codon usage determines the translation rate inEscherichia coli. J. Mol. Biol. 207: 365–377

    PubMed  Google Scholar 

  • Sørensen MA & Pedersen S (1991) Absolutein vivo translation rates of individual codons inEscherichia coli: The two glutamic acid codons, GAA and GAG are translated with a threefold difference in rate. J. Mol. Biol. 222: 265–280

    PubMed  Google Scholar 

  • Stent GS & Brenner S (1961) A genetic locus for the regulation of ribonucleic acid synthesis. Proc. Nat. Acad. Sci. USA 47: 2005–2014

    PubMed  Google Scholar 

  • Tedin K & Bremer H (1992) Toxic effects of the high levels of ppGpp inEscherichia coli are relieved byrpoB mutations. J. Biol. Chem. 267: 2337–2344

    PubMed  Google Scholar 

  • Travers A (1984) Conserved features of coordinately regulatedE. coli promoters. Nucleic Acids Res. 12: 2605–2618

    PubMed  Google Scholar 

  • Vind J, Sørensen MA, Rasmussen MD & Pedersen S (1993) The synthesis of proteins inEscherichia coli is limited by the concentration of free ribosomes: Expression from reporter genes do not always reflect functional mRNA levels. J. Mol. Biol. 231: 678–688

    PubMed  Google Scholar 

  • Vogel U, Pedersen S & Jensen KF (1991) An unusual correlation between ppGpp pool size and the rate of ribosome synthesis during partial pyrimidine starvation ofEscherichia coli. J. Bacteriol. 173: 1168–1174

    PubMed  Google Scholar 

  • Vogel U, Sørensen M, Pedersen S, Jensen KF & Kilstrup M (1992) Decreasing transcription elongation rate inEscherichia coli exposed to amino acid starvation. Mol. Microbiol. 6: 2191–2200

    PubMed  Google Scholar 

  • Wagner EGH, Ehrenberg M & Kurland CG (1982) Kinetic suppression of translational errors by (p)ppGpp. Mol. Gen. Genet. 185: 269–274

    PubMed  Google Scholar 

  • Yoshida M, Travers A & Clark BFC (1972) Inhibition of translation initiation complex formation by MSI. FEBS Lett. 23: 163–166

    PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institute of Microbiology, University of Copenhagen, Øster Farimagsgade 2A, DK-1353, Copenhagen K, Denmark

    Michael A. Sørensen & Steen Pedersen

  2. Institute of Biological Chemistry B, University of Copenhagen, Sølvgade 83, DK-1307, Copenhagen K, Denmark

    Ulla Vogel & Kaj Frank Jensen

Authors
  1. Michael A. Sørensen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ulla Vogel
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kaj Frank Jensen
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Steen Pedersen
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sørensen, M.A., Vogel, U., Jensen, K.F. et al. The rates of macromolecular chain elongation modulate the initiation frequencies for transcription and translation inEscherichia coli . Antonie van Leeuwenhoek 63, 323–331 (1993). https://doi.org/10.1007/BF00871227

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1007/BF00871227

Key words

Search

Navigation