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Chapter 43 : Ribosome-Recycling Factor: an Essential Factor for Protein Synthesis

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Abstract:

This chapter reviews key experimental findings about ribosome-recycling factor (RRF) up to May 1999. RRF is a basic protein with a molecular mass of approximately 20 kDa consisting of 185 amino acids. The molar amount of RRF in a cell is approximately one-half the total molar amount of ribosome, and approximately 30% of total cellular RRF is bound to ribosomes. The ribosome has to be at the termination codon for the release because removal of Asn from the reaction mixture significantly reduced the RRF reaction. In the puromycin-treated polyribosome, each ribosome presumably has an empty A site and bound deacylated tRNA at the P site, a structure similar to that of the posttermination complex. The RRF reaction is dependent on GTP and either elongation factor G (EF-G) or release factor 3 (RF3) in a 1:1 stoichiometric relationship. The important difference between the posttermination complex and the elongation complex is that the former has deacylated tRNA instead of peptidyl-tRNA. This difference leads to disassembly on the one hand and to translocation on the other. In fact, even in the presence of peptidyl-tRNA, RRF may accidentally disassemble the elongating complex. The recycling time of translation was shortened significantly by the addition of RRF and RF3. The bactericidal and bacteriostatic effects of inhibition of RRF suggest that RRF may be an ideal target for antibacterial agents.

Citation: Kaji A, Hirokawa G. 2000. Ribosome-Recycling Factor: an Essential Factor for Protein Synthesis, p 427-539. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch43

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Figure 1

Translational steps involving RRF. (A) Termination complex. (B) Posttermination complex. (C) Unscheduled reinitiation of translation in the absence of RRF. (D) Elongation steps where RRF reduces translational error. Open circles, normal peptide chain; solid circles, peptide chain produced by the unscheduled translation downstream from the termination codon due to the absence of RRF. (Reprinted from , with permission.)

Citation: Kaji A, Hirokawa G. 2000. Ribosome-Recycling Factor: an Essential Factor for Protein Synthesis, p 427-539. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch43
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Image of Figure 2
Figure 2

Conversion of polysomes to monosomes by RRF. (a) Sedimentation profile of polysomes with nascent peptide (labeled with 14C amino acids [open circles]). Solid line represents optical density at 260 nm of fractions measured using ISCO. 1, 2, and 3, are mono-, di-, and trisomes, respectively. (b) Polysomes in panel a treated with puromycin. (c) Polysomes in panel b treated with RRF, EF-G, and GTP. Sedimentation was from left to right in the sucrose gradient centrifugation. (Reprinted from )

Citation: Kaji A, Hirokawa G. 2000. Ribosome-Recycling Factor: an Essential Factor for Protein Synthesis, p 427-539. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch43
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Figure 6

RRF can function in . Complementation of LJ2221 carrying temperature-sensitive RRF at 42°C by RRF. LJ2221 harboring a plasmid (open squares, empty vector pMW118; plus signs, pMO2925 carrying under the control of the promoter) was grown at 32°C to the log phase. At time zero, the culture temperature was shifted to 42°C and the culture was incubated with (plus signs) and without (open squares) the addition of IPTG. The optical density of the culture is plotted against the time after the temperature shift up. (Adapted from )

Citation: Kaji A, Hirokawa G. 2000. Ribosome-Recycling Factor: an Essential Factor for Protein Synthesis, p 427-539. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch43
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Figure 3

Growth curve of LJ14 carrying temperaturesensitive RRF. Triangles, overnight culture (grown at 32°C) diluted and exposed to 43°C at time zero; open squares, same as triangles, but the culture was grown at 32°C; solid circles, same as open squares but the culture was exposed to 43°C at 4 h; solid diamonds, overnight culture not diluted and cultured at 32°C; open diamonds, same as solid diamonds but the culture was exposed to 43°C at time zero. Viable counts were plotted against the time of culture. (Reprinted from )

Citation: Kaji A, Hirokawa G. 2000. Ribosome-Recycling Factor: an Essential Factor for Protein Synthesis, p 427-539. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch43
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Figure 4

In vivo inactivation of temperature-sensitive RRF induces the translation of the reporter gene (-galactosidase) situated in frame downstream from the termination codon of the upstream ORF. The reporter gene, without the initiation signals, is carried by a plasmid, pPEN2363. pPEN2363 is in LJ14 carrying temperature-sensitive RRF (left panel), in wildtype (middle panel), and in LJ14 harboring a plasmid carrying the wild-type (right panel). The culture was grown at 31°C, and the temperature was shifted to 39°C at time zero (solid squares). Open squares control at 31°C. -galactosidase activity is plotted against the time after the temperature shift up. (Reprinted from , with permission.)

Citation: Kaji A, Hirokawa G. 2000. Ribosome-Recycling Factor: an Essential Factor for Protein Synthesis, p 427-539. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch43
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Image of Figure 5
Figure 5

Sequence analysis of 29 RRFs of various species. (A) Average percent identity of each residue expressed as a bar. A horizontal line is drawn at 80% identity. (B) Hydrophilicity of each residue of RRF.

Citation: Kaji A, Hirokawa G. 2000. Ribosome-Recycling Factor: an Essential Factor for Protein Synthesis, p 427-539. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch43
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Figure 7

Plant RRF kills carrying temperature-sensitive (ts) RRF but not wild-type . (A) LJ14 (with tsRRF) harboring a plasmid carrying plant was grown to the stationary phase and diluted at time zero. One culture (solid circles) but not the other (open circles) received IPTG to induce the plant gene at time zero and was incubated at 32°C. An identical experiment was performed with LJ14 carrying the same vector plasmid which was empty (no plant gene) with (closed squares) and without (open squares) IPTG. (B) Identical to panel A except that was wild type. Viable counts were plotted against the time after the addition of IPTG. (Reprinted from , with permission.)

Citation: Kaji A, Hirokawa G. 2000. Ribosome-Recycling Factor: an Essential Factor for Protein Synthesis, p 427-539. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch43
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Tables

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Table 1

Effect of removal of asparagine on release of ribosomebound amB2 R17 RNA and peptide from ribosomes

Citation: Kaji A, Hirokawa G. 2000. Ribosome-Recycling Factor: an Essential Factor for Protein Synthesis, p 427-539. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch43
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Table 2

Release of tRNA from ribosomes during release of ribosomes from mRNA

Citation: Kaji A, Hirokawa G. 2000. Ribosome-Recycling Factor: an Essential Factor for Protein Synthesis, p 427-539. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch43
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Table 3

IF disassembles the complex of 30S subunits with mRNA except for the initiation complex

Citation: Kaji A, Hirokawa G. 2000. Ribosome-Recycling Factor: an Essential Factor for Protein Synthesis, p 427-539. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch43
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Table 4

Stimulation of T4 lysozyme synthesis in vitro by RRF

Citation: Kaji A, Hirokawa G. 2000. Ribosome-Recycling Factor: an Essential Factor for Protein Synthesis, p 427-539. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch43
Generic image for table
Table 5

RRF promotes fidelity of translation

Citation: Kaji A, Hirokawa G. 2000. Ribosome-Recycling Factor: an Essential Factor for Protein Synthesis, p 427-539. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch43

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