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Chapter 42 : Genetic Probes to Bacterial Release Factors: tRNA Mimicry Hypothesis and Beyond

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Genetic Probes to Bacterial Release Factors: tRNA Mimicry Hypothesis and Beyond, Page 1 of 2

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Abstract:

This chapter focuses on the genetic background leading to the ‘‘RF-tRNA mimicry hypothesis’’ and the progress made after its proposal by using genetic probes of bacterial release factors (RFs). It should be a surprising fact that it took more than 30 years after the discovery of the mechanism of sense-codon decoding by tRNA before the authors began to understand the mechanism of stop codon decoding by protein RFs. A major breakthrough in this long-standing coding problem was achieved by the discovery of universally conserved structures in prokaryotic and eukaryotic RFs that led to a novel hypothesis of ‘‘molecular mimicry’’ between RFs and tRNA. An intriguing RF2 variant that acquired omnipotent decoding activity has been isolated as a plasmid-borne mutant that restored the growth of a temperature-sensitive strain of . Of the proposed seven domains of prokaryotic RF1 and RF2, the C-terminal tRNA mimicry portion, including domains D and E, is highly conservative, whereas the N-terminal portion, including domains A and B, is much less conservative. Intriguingly, RF2 is an exception with Thr at this position. Due to this abnormal residue, RF2 terminates translation very weakly at UAA or UGA, and an excess of RF2 was toxic to cells. The RF-tRNA mimicry hypothesis has proven useful to solve the problem of how RF recognizes the stop codon.

Citation: Nakamura Y, Kawazu Y, Uno M, Yoshimura K, Ito K. 2000. Genetic Probes to Bacterial Release Factors: tRNA Mimicry Hypothesis and Beyond, p 519-526. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch42
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Figures

Image of Figure 1
Figure 1

Average similarity plot of prokaryotic RF sequences, including mRF1 (top), and locations of phenotypically important mutations affected in RF2 (bottom). The proposed seven domains A through G are assigned ( ), and the proposed domain functions are indicated. The average similarity score along the entire sequence is shown by the horizontal line. The amino acid position refers to the coordinate of the similarity alignment described ( ), which is distinct from the actual amino acid positions of RF1 and RF2.

Citation: Nakamura Y, Kawazu Y, Uno M, Yoshimura K, Ito K. 2000. Genetic Probes to Bacterial Release Factors: tRNA Mimicry Hypothesis and Beyond, p 519-526. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch42
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Image of Figure 2
Figure 2

Truncated RF1 and RF2 polypeptides possessing the cross-suppression (Csu) activity monitored by the readthrough assay of UAG and UGA alleles in ( ). The positions of alleles are indicated by arrows. a.a., amino acid(s); +, present; –, absent; +/–, weakly present.

Citation: Nakamura Y, Kawazu Y, Uno M, Yoshimura K, Ito K. 2000. Genetic Probes to Bacterial Release Factors: tRNA Mimicry Hypothesis and Beyond, p 519-526. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch42
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Image of Figure 3
Figure 3

RF-ribosome initial binding hypothesis. The predicted sequence of interactions between the ribosome and RF is shown. We propose initial binding to the ribosome of RF preceding stop codon recognition, and mutations may block or interfere with either step 1′ or 2.

Citation: Nakamura Y, Kawazu Y, Uno M, Yoshimura K, Ito K. 2000. Genetic Probes to Bacterial Release Factors: tRNA Mimicry Hypothesis and Beyond, p 519-526. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch42
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Image of Figure 4
Figure 4

Stimulation of the polypeptide release activity of RF1 by variants of RF3 in vitro. f[H]Met release from the f[H]MettRNA•oligonucleotide_ribosome complex upon addition of RF1 and RF3 variants was determined essentially as described previously ( ) except for the messenger oligonucleotide( s). (A) 9-mer minimessenger, 5′-UUC AUG UAA-3′. (B) AUG initiator and UAA terminator triplets. Proteins: 1, RF1 alone; 2, RF1 plus RF3; 3, RF1 plus RF3; 4, RF1 plus RF3; 5, RF1 plus RF3; 6, RF1 plus wild-type RF3. Experiments were performed independently at least seven times, and the values are expressed with standard deviations ( ).

Citation: Nakamura Y, Kawazu Y, Uno M, Yoshimura K, Ito K. 2000. Genetic Probes to Bacterial Release Factors: tRNA Mimicry Hypothesis and Beyond, p 519-526. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch42
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Tables

Generic image for table
Table 1

Mutagenesis of Thr 246 of E. coli RF2

Citation: Nakamura Y, Kawazu Y, Uno M, Yoshimura K, Ito K. 2000. Genetic Probes to Bacterial Release Factors: tRNA Mimicry Hypothesis and Beyond, p 519-526. In Garett R, Douthwaite S, Liljas A, Matheson A, Moore P, Noller H (ed), The Ribosome. ASM Press, Washington, DC. doi: 10.1128/9781555818142.ch42

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