Ribosome traffic in E-coli and regulation of gene expression

The ribosome traffic during translation of E. coli coding sequences was sim ulated, assuming that the rate of translation of individual codons is limit ed by the cognate tRNA availability. Actual translation rates were taken fr om Solomovici et al. (J. theor. Biol. 185, 511-521, 1997). The mean transla tion rates of the 4271 sequences cover a broad, two-fold range, whereas the local rate of translation along messengers varies three-fold on average. T he simulation allows one to sketch the ribosome traffic on the polysome, in particular by providing the extent of mRNA sequences uncovered between con secutive ribosomes and the time during which these sequences are exposed. T hese parameters may participate in the control of mRNA stability and transc riptional 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, an d the times TMAX and TMIN of respectively the slowest and the fastest trans lated 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 belo w TMAX. Both windows display two strong biases, one as expected on the usag e of codon frequencies, and the other surprisingly on the occurrence of ami noacids. (C) 2000 Academic Press.