Fig 1.
Diagram of the ribosome kinetic model.
(A) Illustration of the reaction network that is simulated in the model. Aminoacylation of tRNAs (dashed boxes) indicate an area where there is limited knowledge of the biochemical kinetics and additional experimental work is needed. (B) Overview of the implementation steps. Specific mRNA sequences, and the concentration of ribosomes, are used as input parameters. The program determines the quantities of elongation factors, etc. that are expected from the number of ribosomes based on experimental data [19]. Examples of output data are shown in the final column.
Table 1.
Efficiency of translation for different transcriptomes.
Fig 2.
Translational kinetics of ribosomes at different E. coli growth rates.
Time courses for the percentage of ribosomes (compared with total ribosomal mass) that are initiating (black), elongating (green), terminating (red), stalled (purple), or free 50S (blue) and free 30S:PIC (brown) are shown for growth rates of (A) μ = 0.7, (B) μ = 1.0, and (C) μ = 2.5 doublings per hour. The experimentally expected ratio of ribosome in elongating complexes (70S:EC—green line) to total ribosome is 0.80–0.85 for all growth rates [19], which matches with the model prediction. Time courses represent an average of three separate simulations.
Fig 3.
Peptide chain elongation rates at different E. coli growth rates.
The peptide chain elongation rates (Cp) in amino acids per second are shown for the simulations at growth rates μ = 0.7,1.0, and 2.5 doublings per hour. Running averages of Cp over 1000 seperate protein syntheisis events are given by the red curves and reveal an average peptide chain elongation of Cp = 15,18, and 21 amino acids per second for μ = 0.7,1.0, and 2.5 doublings per hour, respectively. All model predictions of the peptide elongation rates match experimental estimates of [24].
Fig 4.
Percentage of each tRNA in free ternary complex.
For each tRNA listed in Table K in S1 Text, the percentage of the tRNA that is in free ternary complex (TC) is computed by taking the ratio of the amount of the tRNA in free TC to the total amount of the tRNA. The average ratio for each tRNA (over the last 100 seconds of the translational simulation) is shown for for the T07 (black), T10 (red), and T25 (blue and T10a (green) transcriptomes. The tRNAs are ordered from lowest percentage to highest for each simulation separately.
Table 2.
Concentration of tRNAx in free ternary complex.
Fig 5.
Predicted codon decoding times and stalling frequency.
The average codon decoding times a stalling frequencies for each sense codon is calculated from the 215M individual decoding events that occur over the entire transcriptome in 1000s of simulation time. Blue and red bars indicate the T10 and T10a transcriptomes, respectively. Stalling events are computed as the frequency of ribosome stalling that occurs at the given codon.
Table 3.
Efficiency of translation for wild-type E. Coli transcriptomes.
Table 4.
A theoretical estimate for the number of tRNAx in E. Coli. K12.