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Chapter 44 : Mechanism of Bacterial Translation Termination and Ribosome Recycling

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Mechanism of Bacterial Translation Termination and Ribosome Recycling, Page 1 of 2

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Abstract:

The elucidation of the role of release factor 3 (RF3) in translation termination and the demonstration that GTP hydrolysis was needed for RF3 action became possible with the development of improved purified in vitro systems for protein synthesis. In the absence of RF3, the inhibitory action of RF1 on ribosome recycling can be reduced by increasing the ribosome-recycling factor (RRF) concentration, suggesting that whatever the action of RRF may be, it is incompatible with the presence of RF1 on the ribosome. The experiments in vitro with the purified translation system show that ribosome recycling from initiation via protein elongation and termination of protein synthesis depends strictly on the presence of IF3. This implies that RRF and EF-G together split the ribosome into its subunits after termination and that this step is the overture to ribosome recycling back to initiation of translation from the posttermination state. The fate of the mRNA after termination and ribosome recycling is highly relevant for translation of multicistronic mRNAs. The in vitro data suggest that when termination of protein synthesis is followed by the action of RRF, EF-G, and IF3 the 30S particle remains attached to the mRNA, allowing the latter to diffuse long distances along the subunit. In the presence of GTP, RF3 accelerates recycling of RF1 and RF2 by enhancing their rates of dissociation after termination of translation.

Citation: Ehrenberg M, Dincbas V, Freistroffer D, Heurgué-Hamard V, Karimi R, Pavlov M, Buckingham R. 2000. Mechanism of Bacterial Translation Termination and Ribosome Recycling, p 541-552. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch44

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Image of Figure 1
Figure 1

Stimulation of RF1 recycling by RF3. Termination complex containing fMet-Phe-Thr-Ile-tRNA bound in the P site with a UAA codon in the A site was prepared as described by Freistroffer et al. (1997). (A) The amount of peptidyl-tRNA remaining bound to ribosomes after 2 min of incubation with RF1, with and without 0.9 μM RF3 and with or without 0.2 mM GTP, is shown as a function of the amount of RF1 present. (B) The amount of peptidyl-tRNA remaining bound to ribosomes after incubation with 0.25 pmol of RF1 is shown as in panel A as a function of time of incubation. Stimulation of RF1 recycling is seen to require the presence of GTP. The data are from Freistroffer et al., 1997.

Citation: Ehrenberg M, Dincbas V, Freistroffer D, Heurgué-Hamard V, Karimi R, Pavlov M, Buckingham R. 2000. Mechanism of Bacterial Translation Termination and Ribosome Recycling, p 541-552. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch44
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Image of Figure 2
Figure 2

Rapid recycling of ribosomes requires RF3, RRF, and EF-G. Ribosome-recycling times for the translation of a short mRNA encoding fMet-Phe-Leu were measured in vitro as described by and are shown at the right of each horizontal bar in seconds. For purposes of interpretation, the overall recycling time in the presence of all components is divided arbitrarily into equal periods for initiation, elongation and release, RF release, and the remaining events in ribosome recycling. The horizontal bars interpret the increased recycling time when RRF, RF3, or both factors are omitted in terms of increased times required for RF release and/or ribosome recycling. The two lowest bars show the effect of reducing the concentration of EF-G from 0.8 to 0.3 μM, which increases the overall recycling time in the presence but not in the absence of RRF. The data are from .

Citation: Ehrenberg M, Dincbas V, Freistroffer D, Heurgué-Hamard V, Karimi R, Pavlov M, Buckingham R. 2000. Mechanism of Bacterial Translation Termination and Ribosome Recycling, p 541-552. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch44
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Image of Figure 3
Figure 3

RRF restores rapid ribosome recycling inhibited by high concentration of RF1. Ribosome-recycling times for the synthesis of fMet-Phe-Leu were measured in vitro as described by at three concentrations of RF1 in the absence of RF3. The recycling times are shown as functions of the reciprocal of the RRF concentration present in the translation system. The data, drawn from , show that the increase in recycling time due to RF1 rebinding to the posttermination complex can be countered by increasing the concentration of RRF in the translation system.

Citation: Ehrenberg M, Dincbas V, Freistroffer D, Heurgué-Hamard V, Karimi R, Pavlov M, Buckingham R. 2000. Mechanism of Bacterial Translation Termination and Ribosome Recycling, p 541-552. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch44
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Figure 4

RRF, EF-G, and IF3 release deacylated tRNA from the posttermination complex. Termination complexes containing fMet-Phe-Thr-Ile-tRNA bound in the P site with a UAA codon in the A site were prepared as described by , and the tetrapeptide was released by reaction with puromycin. The dissociation of deacylated tRNA was monitored by incubation of the posttermination complexes in the presence of an excess of Ile-tRNA synthetase and other components needed for the rapid aminoacylation of tRNAwith [C]Ile, with or without the addition of factors RRF, EF-G, IF3, and RF3 as shown. The data are from Karimi et al., 1999.

Citation: Ehrenberg M, Dincbas V, Freistroffer D, Heurgué-Hamard V, Karimi R, Pavlov M, Buckingham R. 2000. Mechanism of Bacterial Translation Termination and Ribosome Recycling, p 541-552. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch44
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Image of Figure 5
Figure 5

RRF and EF-G are required for recycling of the 50S ribosomal subunit, and IF3 is required for recycling of the 30S ribosomal subunit. The synthesis of fMet-Phe-Thr-Ile was measured as described by . The translation system contained a constant amount (6 pmol) of active preinitiated 30S subunits and different amounts of active 50S subunits as indicated and as shown by the upper limits of the light-gray (30S) and medium-gray (50S) shaded areas. The experiments were carried out in the absence of RRF and IF3 (○), with 1 μM RRF (△), and with 1 μM (each) of RRF and IF3 (◇). In the absence of RRF and IF3, the amount of tetrapeptide synthesized is limited by the amount of 50S subunit added. In the presence of RRF (and EF-G) but the absence of IF3, the amount of tetrapeptide synthesized is limited by the amount of preinitiated 30S subunits, showing that under these conditions the 50S subunit can recycle. In the presence of both RRF (and EF-G) and IF3, the amount of tetrapeptide synthesized becomes greater than the amount of preinitiated 30S subunits, indicating that both subunits can recycle. The data are from Karimi et al., 1999.

Citation: Ehrenberg M, Dincbas V, Freistroffer D, Heurgué-Hamard V, Karimi R, Pavlov M, Buckingham R. 2000. Mechanism of Bacterial Translation Termination and Ribosome Recycling, p 541-552. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch44
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Image of Figure 6
Figure 6

IF3 removes deacylated tRNA from the 30S subunit. 30S ribosomal subunits were programmed with a short mRNA encoding fMet-Phe-Leu and with deacylated tRNA in the P site, as described by . The complexes were then incubated in the absence of RRF, EF-G, and IF3 (○), with 1 μM RRF and 1 μM EF-G (△), with 1 μM IF3 (◇), and with 1 μM RRF, 1 μM EF-G, and 1 μM IF3 (□).The dissociation of deacylated tRNA was monitored by charging the tRNA in the presence of an excess of Phe-tRNA synthetase, [C]Phe, and other components needed for rapid aminoacylation. The data are from Karimi et al., 1999.

Citation: Ehrenberg M, Dincbas V, Freistroffer D, Heurgué-Hamard V, Karimi R, Pavlov M, Buckingham R. 2000. Mechanism of Bacterial Translation Termination and Ribosome Recycling, p 541-552. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch44
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Image of Figure 7
Figure 7

Model for the events following peptide release. RF3 catalyzes the dissociation of RF1 (or RF2) from the A site after peptide release ( ). RRF and EF-G then bind to the 70S posttermination complex and, in a GTPrequiring reaction, provoke the dissociation of the 50S subunit. Finally, IF3 displaces the deacylated tRNA from the 30S posttermination complex ( ).

Citation: Ehrenberg M, Dincbas V, Freistroffer D, Heurgué-Hamard V, Karimi R, Pavlov M, Buckingham R. 2000. Mechanism of Bacterial Translation Termination and Ribosome Recycling, p 541-552. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch44
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Image of Figure 8
Figure 8

Stimulation of RF2 recycling by RF3 in the presence of different guanine nucleotides. A catalytic amount of RF2 (10 mM) was added to termination complexes (90 nM) containing fMet-Phe-Thr-Ile-tRNA bound in the P sites of ribosomes with a UGA(U) stop signal in the A site, and the fraction of the released fMet-Phe-Thr-Ile tetrapeptide was measured as a function of time. RF3 (0.9 μM) and guanine nucleotides (0.2 mM) were added where indicated. The figure shows that the rate of RF2 recycling in the presence of GTP (○) is much faster than with GDPNP (◇) and that RF3 added with GDP (△) is slightly stimulatory. In contrast, RF3 added without guanine nucleotide (□) inhibits RF2 recycling compared to the control in the absence of RF3 (▲).

Citation: Ehrenberg M, Dincbas V, Freistroffer D, Heurgué-Hamard V, Karimi R, Pavlov M, Buckingham R. 2000. Mechanism of Bacterial Translation Termination and Ribosome Recycling, p 541-552. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch44
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