Fig 1.
Ribosome and EF-Tu as targets for protein synthesis inhibition.
After a tRNA (gray sphere) is released from a ribosome (gray dome), it binds to an aminoacyl-tRNA synthetase (violet box) that recharges the tRNA with its cognate amino acid (green sphere). Under physiological conditions, the recharged tRNA binds to elongation factor EF-Tu (blue sphere) to form a ternary complex that delivers its amino acid to a translating ribosome. If EF-Tu gets inhibited, e.g., by an antibiotic or toxin, it is no longer able to bind aminoacylated tRNAs (A). Alternatively, protein synthesis and, thus, cellular growth can be impeded through ribosome inhibition (B) or via simultaneous inhibition of ribosomes and EF-Tu (C). See Table 1 for more details on the different inhibition pathways.
Table 1.
Some examples for reported mechanisms of translation inhibition targeting the ribosome and/or EF-Tu as illustrated in Fig 1, with no claim to completeness.
Fig 2.
Ultrasensitive dependence of the overall elongation rate on EF-Tu concentration in E. coli.
A) Theoretical predictions for E. coli growing at a specific growth rate of 2.5 h−1 with a physiological EF-Tu concentration of about 250 μM (blue dashed line) [32]. If the EF-Tu concentration is reduced by 15% (orange dashed line), the overall elongation rate strongly decreases by about 50%. When 20% of all EF-Tu molecules are inhibited (red dashed line), a critical EF-Tu concentration is reached, at which protein synthesis is almost completely suppressed. B) Experimental data from van der Meide (Fig. 3 in Ref. [30]), showing an ultrasensitive dependence of the overall elongation rate on EF-Tu for most of the studied E. coli strains. To facilitate comparison, data are rescaled as described in S1 Text and solid lines are drawn as a guide to the eye (no model fitting). Symbols represent different E. coli strains with mutated tufA and/or tufB genes coding for EF-Tu, see Table 2 in Ref. [30].
Fig 3.
Ultrasensitivity in reduced translation systems.
A) Inhibition of EF-Tu generally leads to a decrease in the overall elongation rate. For the one-codon-one-tRNA (1C-1T) translation system (solid blue line), the overall elongation rate is proportional to the abundance of EF-Tu for low EF-Tu concentrations. The same holds for the 2C-2T translation system when codon usages pi and tRNA concentrations Xi (i = 1, 2) are perfectly balanced (dashed orange line; p1/p2 = X1/X2 = 1). If the codon usages do not exactly match the relative tRNA concentrations, the overall elongation rate becomes ultrasensitive to the concentration of EF-Tu (green, red, and purple dashed lines; p1/p2 = 1 and X1/X2 as indicated). In all cases, the total tRNA concentration is X1 + X2 = 344 μM. Vertical solid black lines indicate EF-Tu threshold concentrations , 138 μM and 206 μM, respectively, as given by Eq (1). B) Concentrations of free EF-Tu molecules (solid lines), free ternary complexes of the more abundant species 1 (dotted lines) and of the less abundant species 2 (dashed lines) as determined by the set of Eqs. (18)—(21) in S1 Text. In the low-concentration regime
, the free ternary complex concentration of the more abundant species 1 increases roughly linearly with
whereas the concentration of the less abundant species 2 remains practically zero up to
(see also S3 and S4 Figs). Same parameters and corresponding color code as in A). C) PURE system simulator [31]: Quasi-steady state overall elongation rate of in-vitro fMetLysHis tripeptide synthesis as a function of EF-Tu concentration for XLys + XHis = 3.44 μM and XLys/XHis as indicated, see text for details. Vertical solid black lines indicate EF-Tu threshold concentrations determined by Eq (1). D) Response of the in-vitro fMetLysHis tripeptide synthesis system to a sudden drop in EF-Tu concentration from 5 μM to 3 μM at 100s after start of reaction as predicted by the PURE system simulator for tRNA concentrations XLys + XHis = 3.44 μM and XLys/XHis = 8/2.
Fig 4.
PURE system simulator: Effects of ribosome (and EF-Tu) inhibition on the synthesis of fMetLysHis tripeptides.
When the simulated PURE system is depleted for ribosomes (solid lines), the total rate of peptide synthesis decreases (purple) but the synthesis rate per ribosome increases as long as the ribosomal concentration is not too low (black). In contrast, Fig 3C) shows that upon depletion of EF-Tu (i.e., for constant concentration of ribosomes), both the peptide synthesis rate in total and per ribosome decrease. When the concentrations of ribosomes and EF-Tu molecules are inhibited simultaneously by the same absolute amounts (diamonds, [EF-Tu] = [ribosomes]), EF-Tu inhibition has a stronger influence on peptide synthesis than ribosome inhibition (A, B) unless the tRNA concentrations are comparable (C, D). For each data point, translation was simulated until a quasi-steady state was reached. Simulations were performed and parameterized as described in the Methods, with a total tRNA concentration of XLys + XHis = 3.44 μM and concentration ratios XLys/XHis as indicated.