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Chapter 40 : Factor-Mediated Termination of Protein Synthesis: a Welcome Return to the Mainstream of Translation

Authors: Daniel N. Wilson1, Lousie L. Major1, John B. Mansell1, Warren P. Tate1, Mark E. Dalphin2, Herman J. Pel3
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Affiliations: 1: Department of Biochemistry and Centre for Gene Research, University of Otago, PO Box 56, Dunedin, New Zealand; 2: Amgen Inc., Amgen Center, Thousand Oaks, CA91320-1799; 3: DSM Food Specialities, DSM Gist 426-0295, P.O. Box 1, 2600 MA Delft, The Netherlands
Content Type: Monograph
Publication Year: 2000

Category: Microbial Genetics and Molecular Biology

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Abstract:

Termination is beginning to resemble a typical translation mechanism with parallels to other phases of protein synthesis. Concepts such as structural mimicry between the complexes formed at each stage of protein synthesis emphasize this change in perception. This chapter focuses on how the information gathered principally since the last ribosome meeting has enhanced one's understanding of the termination phase of protein synthesis. RF3 has been shown to enhance the efficiency of decoding of stop signals and in particular the signals that are used by highly expressed genes. This suggests that when bacteria require high rates of translation and efficient decoding of stop signals, RF3 makes an important contribution to the translational efficiency. The structure of IF1 has been determined by nuclear magnetic resonance spectroscopy and is classified as a member of an oligomer binding (OB)-fold family of proteins, based on the ability of this structure to bind oligosaccharides and oligonucleotides. The discovery of recoding provided examples of stop codons regularly failing to terminate protein synthesis, such as at the RF2 frameshift site. The discovery that RF3 was a translational G protein was puzzling, considering early work which examined the effect of guanine nucleotides on RF3 activity. The disassembly of the termination complex in prokaryotes was shown almost 30 years ago to involve two factors, a ribosome-releasing factor, now called ribosome-recycling factor (RRF), and EF-G.

Citation: Wilson D, Major L, Mansell J, Tate W, Dalphin M, Pel H. 2000. Factor-Mediated Termination of Protein Synthesis: a Welcome Return to the Mainstream of Translation, p 495-508. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch40
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Factor-Mediated Termination of Protein Synthesis: a Welcome Return to the Mainstream of Translation
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Citation: Wilson D, Major L, Mansell J, Tate W, Dalphin M, Pel H. 2000. Factor-Mediated Termination of Protein Synthesis: a Welcome Return to the Mainstream of Translation, p 495-508. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch40
/content/10.1128/9781555818142.chap40.fig40-1
Figure 1

Sequence alignment of the region encompassing the RF type-specific sequences (positions 190 to 217) of selected prokaryotic RFs. Conserved (black boxes) and similar (light gray boxes with black text) residues between all RFs and conserved residues specific for each RF type (dark gray boxes with white text) are presented. Mutations (a to f) clustered within this region are documented in Table 1 . The abbreviations are defined in the legend to Fig. 2, except the following: Bfi, ; Hpy, ; Bbu, ; and Tth, .

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Figure 1

Sequence alignment of the region encompassing the RF type-specific sequences (positions 190 to 217) of selected prokaryotic RFs. Conserved (black boxes) and similar (light gray boxes with black text) residues between all RFs and conserved residues specific for each RF type (dark gray boxes with white text) are presented. Mutations (a to f) clustered within this region are documented in Table 1 . The abbreviations are defined in the legend to Fig. 2, except the following: Bfi, ; Hpy, ; Bbu, ; and Tth, .

Citation: Wilson D, Major L, Mansell J, Tate W, Dalphin M, Pel H. 2000. Factor-Mediated Termination of Protein Synthesis: a Welcome Return to the Mainstream of Translation, p 495-508. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch40
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Figure 2

Similarity between prokaryotic and organellar IF1s and class I RFs. The two types of class I RFs, RF1 and RF2, have been considered as separate families, since their stop codon specificities (UAA and UAG for RF1; UAA and UGA for RF2) suggest that significant deviations may exist in their interactions with mRNA and the decoding site. (A) Positions of amino acids identical among all currently available prokaryotic and organellar RFs (all RFs), RF1s (RF1), RF2s (RF2), and IF1s (IF1) are indicated by vertical bars. The alignments were accomplished with the PILEUP program (GCG package, University of Wisconsin Genetics Computer Group). (B) Alignment of distantly related members of the IF1 and RF families. IF1 and RF amino acid residues that are identical or functionally related in at least three IF1s and three RF1s or two RF2s are indicated. The following sets of amino acids are considered to be functionally related: A and G; S, T, and C; L, I, V, M, and F; F, Y, W, and H; K and R; D and E; D and N; and E and Q. Abbreviations: Bsu, ; Cbu, ; Ctr, ; Eco, ; Hin, ; Lla, ; Mbo, ; Mca, ; Mge, ; Mle, ; Mpn, ; Mpo, ; Mtu, . cZma, cSol, cNta, cOsa, cEvi, and cPth are chloroplast IF1s of , , , , , and , respectively.

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Figure 2

Similarity between prokaryotic and organellar IF1s and class I RFs. The two types of class I RFs, RF1 and RF2, have been considered as separate families, since their stop codon specificities (UAA and UAG for RF1; UAA and UGA for RF2) suggest that significant deviations may exist in their interactions with mRNA and the decoding site. (A) Positions of amino acids identical among all currently available prokaryotic and organellar RFs (all RFs), RF1s (RF1), RF2s (RF2), and IF1s (IF1) are indicated by vertical bars. The alignments were accomplished with the PILEUP program (GCG package, University of Wisconsin Genetics Computer Group). (B) Alignment of distantly related members of the IF1 and RF families. IF1 and RF amino acid residues that are identical or functionally related in at least three IF1s and three RF1s or two RF2s are indicated. The following sets of amino acids are considered to be functionally related: A and G; S, T, and C; L, I, V, M, and F; F, Y, W, and H; K and R; D and E; D and N; and E and Q. Abbreviations: Bsu, ; Cbu, ; Ctr, ; Eco, ; Hin, ; Lla, ; Mbo, ; Mca, ; Mge, ; Mle, ; Mpn, ; Mpo, ; Mtu, . cZma, cSol, cNta, cOsa, cEvi, and cPth are chloroplast IF1s of , , , , , and , respectively.

Citation: Wilson D, Major L, Mansell J, Tate W, Dalphin M, Pel H. 2000. Factor-Mediated Termination of Protein Synthesis: a Welcome Return to the Mainstream of Translation, p 495-508. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch40
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Figure 3

Dot blot of IF1 against RF2 and RF3 against EFG. The full sequences of IF1 (positions 1 to 71) and RF2 (1 to 366) (A) and RF3 (1 to 527) and EF-G (1 to 703) (B) were compared to determine regions of similarity by using the Genetics Computer Group programs Compare and Dotplot. Dotplot was run at a density of 306.67. The alignments were performed with a stringency value of 15.

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Figure 3

Dot blot of IF1 against RF2 and RF3 against EFG. The full sequences of IF1 (positions 1 to 71) and RF2 (1 to 366) (A) and RF3 (1 to 527) and EF-G (1 to 703) (B) were compared to determine regions of similarity by using the Genetics Computer Group programs Compare and Dotplot. Dotplot was run at a density of 306.67. The alignments were performed with a stringency value of 15.

Citation: Wilson D, Major L, Mansell J, Tate W, Dalphin M, Pel H. 2000. Factor-Mediated Termination of Protein Synthesis: a Welcome Return to the Mainstream of Translation, p 495-508. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch40
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Figure 4

Predicted structure of RF3 based on threading analyses with EF-G. The predicted structure of RF3 is compared with the known three-dimensional structure of EF-G. Threading of RF3 sequences onto EF-G was performed with Swiss-Model ( ).

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Figure 4

Predicted structure of RF3 based on threading analyses with EF-G. The predicted structure of RF3 is compared with the known three-dimensional structure of EF-G. Threading of RF3 sequences onto EF-G was performed with Swiss-Model ( ).

Citation: Wilson D, Major L, Mansell J, Tate W, Dalphin M, Pel H. 2000. Factor-Mediated Termination of Protein Synthesis: a Welcome Return to the Mainstream of Translation, p 495-508. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch40
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Figure 5

The 3A' reporter system was used to analyze the upstream and downstream context effects on translations termination. (A) Sequences that were predicted to provide a strong or weak context were placed upstream (5') and downstream (3') of the stop codon (in this case, UGA). The termination signals were placed between the second and third A' domains in the 3A' reporter plasmid. Expression from this plasmid generates two potential products, a termination product (14 kDa) and a readthrough product (21 kDa), which can be separated on the basis of size. (B) Expression of the 3A' reporter plasmid containing UGA stop signals in wild-type (white) and suppressor (black) tRNA strains is presented as percent readthrough. Combinations of strong (S) and weak (W) upstream and downstream contexts are illustrated (for example, a strong upstream and weak downstream signal is S-UGA-W). The error bars indicate standard errors of the mean.

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Figure 5

The 3A' reporter system was used to analyze the upstream and downstream context effects on translations termination. (A) Sequences that were predicted to provide a strong or weak context were placed upstream (5') and downstream (3') of the stop codon (in this case, UGA). The termination signals were placed between the second and third A' domains in the 3A' reporter plasmid. Expression from this plasmid generates two potential products, a termination product (14 kDa) and a readthrough product (21 kDa), which can be separated on the basis of size. (B) Expression of the 3A' reporter plasmid containing UGA stop signals in wild-type (white) and suppressor (black) tRNA strains is presented as percent readthrough. Combinations of strong (S) and weak (W) upstream and downstream contexts are illustrated (for example, a strong upstream and weak downstream signal is S-UGA-W). The error bars indicate standard errors of the mean.

Citation: Wilson D, Major L, Mansell J, Tate W, Dalphin M, Pel H. 2000. Factor-Mediated Termination of Protein Synthesis: a Welcome Return to the Mainstream of Translation, p 495-508. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch40
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Tables

Factor-Mediated Termination of Protein Synthesis: a Welcome Return to the Mainstream of Translation
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Citation: Wilson D, Major L, Mansell J, Tate W, Dalphin M, Pel H. 2000. Factor-Mediated Termination of Protein Synthesis: a Welcome Return to the Mainstream of Translation, p 495-508. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch40
/content/10.1128/9781555818142.chap40.tab40-1
Table 1

Characterized mutations in bacterial RF1 and RF2

Generic image for table
Table 1

Characterized mutations in bacterial RF1 and RF2

Citation: Wilson D, Major L, Mansell J, Tate W, Dalphin M, Pel H. 2000. Factor-Mediated Termination of Protein Synthesis: a Welcome Return to the Mainstream of Translation, p 495-508. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch40

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