Translation is a non-uniform process. Effect of tRNA availability on the rate of elongation of nascent polypeptide chains.

We reported elsewhere (Varenne et al., 1982) that, during synthesis of a number of colicins in Escherichia coli, intermediate nascent chains of discrete sizes accumulated, suggesting a variable rate of translation. In this paper, a detailed analysis provides arguments that this phenomenon, at least for the proteins under study, is not related to aspects of messenger RNA such as secondary structure. It is linked to the difference in transfer RNA availability for the various codons. Experimental analysis of translation of other proteins in E. coli confirms that the main origin for the discontinuous translation in the polypeptide elongation cycle is the following. For a given codon, the stochastic search of the cognate ternary complex (aminoacyl-tRNA-EF-Tu-GTP) is the rate-limiting step in the elongation cycle: transpeptidation and translocation steps are much faster. The degree of slackening in ribosome movement is almost proportional to the inverse of tRNA concentrations. The verification of this model and its possible physiological significance are discussed.

[1]  B. Lugtenberg,et al.  Complete nucleotide sequence of phoE, the structural gene for the phosphate limitation inducible outer membrane pore protein of Escherichia coli K12. , 1983, Journal of molecular biology.

[2]  C. Yanofsky.  Attenuation in the control of expression of bacterial operons , 1981, Nature.

[3]  H. Aiba,et al.  Molecular cloning and nucleotide sequencing of the gene for E. coli cAMP receptor protein. , 1982, Nucleic acids research.

[4]  Douglas R. Smith,et al.  Nucleotide sequence of the E. coli gene coding for dihydrofolate reductase , 2022 .

[5]  I. Zabin,et al.  Beta-galactosidase. Rates of synthesis and degradation of incomplete chains. , 1972, The Journal of biological chemistry.

[6]  J. Clément,et al.  Gene sequence of the λ receptor, an outer membrane protein of E. coli K12 , 1981, Cell.

[7]  T. Ikemura.  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. , 1981, Journal of molecular biology.

[8]  W. Herlihy,et al.  Primary structure of a large aminoacyl-tRNA synthetase. , 1981, Science.

[9]  M. Gouy,et al.  Polypeptide elongation and tRNA cycling in Escherichia coli: A dynamic approach , 1980, FEBS letters.

[10]  J. Garel,et al.  Does quantitative tRNA adaptation to codon content in mRNA optimize the ribosomal translation efficiency? Proposal for a translation system model. , 1981, Biochimie.

[11]  F. Boogerd,et al.  Limited proteolysis of cloacin DF13 and characterization of the cleavage products. , 1978, Biochemistry.

[12]  The nucleotide sequence of the structural gene for Escherichia coli tryptophanyl-tRNA synthetase. , 1982, The Journal of biological chemistry.

[13]  R. Swank,et al.  Molecular weight analysis of oligopeptides by electrophoresis in polyacrylamide gel with sodium dodecyl sulfate. , 1971, Analytical biochemistry.

[14]  R. Lloubès,et al.  Nucleotide sequence of the gene for the immunity protein to colicin A. Analysis of codon usage of immunity proteins as compared to colicins. , 1984, European journal of biochemistry.

[15]  C. M. Joyce,et al.  Nucleotide sequence of the Escherichia coli polA gene and primary structure of DNA polymerase I. , 1982, The Journal of biological chemistry.

[16]  Gel chromatographic analysis of nascent globin chains. Evidence of nonuniform size distribution. , 1974, The Journal of biological chemistry.

[17]  M. Inouye,et al.  Gene structure of the OmpA protein, a major surface protein of Escherichia coli required for cell-cell interaction. , 1980, Journal of molecular biology.

[18]  J. Darlix,et al.  Discontinuous in vitro transcription of DNA. , 1972, Biochimie.

[19]  G. von Heijne,et al.  Models for mRNA translation: theory versus experiment. , 1978, European journal of biochemistry.

[20]  Yu A. Ovchinnikov,et al.  The primary structure of E. coli RNA polymerase, Nucleotide sequence of the rpoC gene and amino acid sequence of the beta'-subunit , 1982, Nucleic Acids Res..

[21]  L. Josefsson,et al.  Different exported proteins in E. coli show differences in the temporal mode of processing in vivo , 1981, Cell.

[22]  C. Yanofsky,et al.  Nucleotide sequence of the structural gene for tryptophanase of Escherichia coli K-12 , 1981, Journal of bacteriology.

[23]  T. Ikemura.  Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. , 1981, Journal of molecular biology.

[24]  K. Imahori,et al.  Assignment of the functional loci in colicin E2 and E3 molecules by the characterization of their proteolytic fragments. , 1980, Biochemistry.

[25]  D. Kennell,et al.  Evidence for variable rates of ribosome movement in Escherichia coli. , 1976, Journal of molecular biology.

[26]  C. Lazdunski,et al.  Biosynthesis and export of colicin A in Citrobacter freundii CA31. , 1981, European journal of biochemistry.

[27]  C. Lazdunski,et al.  Variable rate of polypeptide chain elongation for colicins A, E2 and E3. , 1982, Journal of molecular biology.

[28]  K. Otto,et al.  Sequence of the lacZ gene of Escherichia coli. , 1983, The EMBO journal.

[29]  H. Lodish,et al.  A kinetic model of protein synthesis. Application to hemoglobin synthesis and translational control. , 1979, The Journal of biological chemistry.

[30]  P. Cossart,et al.  Cloning and sequence of the crp gene of Escherichia coli K 12. , 1982, Nucleic acids research.

[31]  T. Ikemura.  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. , 1982, Journal of molecular biology.

[32]  W. Fiers,et al.  Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. , 1982, Gene.

[33]  M. Gouy,et al.  Codon usage in bacteria: correlation with gene expressivity. , 1982, Nucleic acids research.

[34]  W. Fiers,et al.  Nucleotide Sequence of the Gene Coding for the Bacteriophage MS2 Coat Protein , 1972, Nature.

[35]  P. Cossart,et al.  Nucleotide sequence of the thrB gene of E. coli, and its two adjacent regions; the thrAB and thrBC junctions. , 1981, Nucleic acids research.

[36]  A. Grossman,et al.  Mutations in the Lon gene of E. coli K12 phenotypically suppress a mutation in the sigma subunit of RNA polymerase , 1983, Cell.

[37]  M. Chamberlin,et al.  Pausing and attenuation of in vitro transcription in the rrnB operon of E. coli , 1981, Cell.

[38]  J. Manley.  Synthesis and degradation of termination and premature-termination fragments of β-galactosidase in vitro and in vivo , 1978 .

[39]  Manolo Gouy,et al.  Codon catalog usage is a genome strategy modulated for gene expressivity , 1981, Nucleic Acids Res..

[40]  A. Morris,et al.  Nonuniform size distribution of nascent peptides. The effect of messenger RNA structure upon the rate of translation. , 1979, Archives of biochemistry and biophysics.

[41]  M. Gouy,et al.  Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. , 1980, Nucleic acids research.

[42]  R. Laskey,et al.  Quantitative film detection of 3H and 14C in polyacrylamide gels by fluorography. , 1975, European journal of biochemistry.

[43]  C. Lazdunski,et al.  Complete nucleotide sequence of the structural gene for colicin A, a gene translated at non-uniform rate. , 1983, Journal of molecular biology.