Ribosome traffic in E. coli and regulation of gene expression.

The ribosome traffic during translation of E. coli coding sequences was simulated, assuming that the rate of translation of individual codons is limited by the cognate tRNA availability. Actual translation rates were taken from Solomovici et al. (J. theor. Biol. 185, 511-521, 1997). The mean translation rates of the 4271 sequences cover a broad, two-fold range, whereas the local rate of translation along messengers varies three-fold on average. The simulation allows one to sketch the ribosome traffic on the polysome, in particular by providing the extent of mRNA sequences uncovered between consecutive ribosomes and the time during which these sequences are exposed. These parameters may participate in the control of mRNA stability and transcriptional polarity. By averaging the translation rates in a 17-codon window, assumed to be the sequence covered by a translating ribosome, and sliding this window along a given coding sequence, the addresses KMAX and KMIN, and the times TMAX and TMIN of respectively the slowest and the fastest translated window were determined. It is shown that under the assumptions made, TMAX sets the number of proteins translated from a given mRNA molecule per unit time, in case the delay between consecutive translation starts is below TMAX. Both windows display two strong biases, one as expected on the usage of codon frequencies, and the other surprisingly on the occurrence of amino acids.

Does Escherichia coli optimize the economics of the translation process?

The codon translation rate is usually assumed to be proportional to the cellular concentration of the cognate tRNA, but synonymous codons sharing the same cognate tRNA may be translated at rather different rates. To account for the latter observation, we assume that the translation process is optimized in two respects: (i), the codon demand is optimized with respect to the supply of cognate tRNAs (composition of the tRNA pool); and (ii), for synonymous codons sharing the same cognate tRNA, the usage frequency of each codon correlates optimally with the stability of the codon-anticodon complex. These assumptions allow us to compute the relative rate constants of synonymous codons. Highly expressed genes, which produce 80-90% of the protein mass in the E. coli cell, appear to have selected codons which make an optimal use of the tRNA pool. Assuming the optimization criteria were valid, a list of codon translation times (in ms) were derived from available experimental data.