The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli.

Poole, Elizabeth S.; Brown, C. M.

doi:10.1002/j.1460-2075.1995.tb06985.x

Cited by 247 publications

(206 citation statements)

References 54 publications

(41 reference statements)

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“…The mRNA bases following the stop codon can also be cross-linked to RF2, implying the release factor has a footprint broader than a single codon span (Poole et al, 1998). Consistent with this, 3h nucleotide stop codon context has a marked influence on the efficiency of stop codon recognition in bacteria, yeast and human cells (Poole et al, 1995 ; Bonetti et al, 1995 ; McCaughan et al, 1995). In prokaryotes, dissociation of RF1 and RF2 from the ribosome is stimulated by the addition of a GTPase release factor, RF3, analogous to eukaryote eRF3 (Freistroffer et al, 1997).…”

Section: The Translation Termination Apparatus In Eukaryotes and Prokmentioning

confidence: 93%

“…The stop codon then has characteristics of a tetranucleotide, where the identity of the fourth base determines the efficiency with which termination occurs. Contexts favouring termination are predominantly used by highly expressed genes in all micro-organisms so far examined (Bonetti et al, 1995 ;Poole et al, 1995). Conversely, viral genomes containing stop codons whose suppression is required to direct translation of extended proteins have stop codons in poor contexts, favouring suppression.…”

Section: The Termination Signal : Stop Codons and The Role Of Flankinmentioning

confidence: 99%

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Endless possibilities: translation termination and stop codon recognition

et al. 2001

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OverviewThe process of protein synthesis can be divided into three main phases : initiation, during which the ribosomal subunits join the mRNA and locate the AUG initiator codon ; elongation, during which sense codons are decoded and the bulk of the polypeptide is made ; and termination, during which a stop codon directs the release of the completed polypeptide from the ribosome. Whereas the general principles of sense codon decoding by transfer RNAs are well established, a clear picture of translation termination and stop codon recognition has hitherto been lacking. Recently however, the use of optimized, complex, reconstituted in vitro termination reactions to identify the roles of key termination factors, and the solution of tertiary structures of termination factors, has allowed a reappraisal of termination factor structure and function. This review will describe these recent advances, many of which have resulted from studies of termination in micro-organisms, and in the light of the new information, discuss models for the mechanism of termination and recognition of the stop codon. While the mechanism of peptide chain termination is normally effective, stop codons are not always recognized efficiently, and during the translation of certain viral RNAs can be suppressed or read through, resulting in the expression of additional coding information. How stop codons are reassigned to encode ' sense ' at a given frequency in some RNAs will be reviewed in the context of current understanding of termination and stop codon recognition mechanisms. The translation termination apparatus in eukaryotes and prokaryotesDuring translation termination, a stop codon located in the ribosomal A-site is recognized by a release factor or release factor complex, which binds the ribosome and triggers release of the nascent peptide. In eukaryotes, translation is terminated by a heterodimer consisting of two proteins, release factors eRF1 and eRF3, which interact in vivo (Frolova et al., 1994 ;Zhouravleva et al., 1995 ;Stansfield et al., 1995). eRF1 recognizes all three stop codons and triggers peptidyl-tRNA hydrolysis by the ribosome, releasing the nascent peptide (Frolova et al., 1994 ; Drugeon et al., 1997). Eukaryote termination efficiency is enhanced by the GTPase release factor eRF3, the second component of the heterodimer eRF complex. In response to a stop codon in the ribosomal A-site, formation of a quaternary complex comprising the ribosome, eRF1, GTP and eRF3 triggers GTP hydrolysis and enhances the rate of peptidyl release (Zhouravleva et al., 1995 ; Frolova et al., 1994 ; Fig. 1). In yeast, eRF1 and eRF3 are encoded by essential genes (SUP35 and SUP45, respectively), mutations in which produce nonsense suppression phenotypes (Stansfield & Tuite, 1994).In contrast to eukaryotes, the role of stop codon recognition during translation termination in eubacteria is divided between two so-called class 1 release factors, RF1 and RF2, which in Escherichia coli are encoded by the essential prfA and prfB genes, respectively (Scolni...

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Section: The Translation Termination Apparatus In Eukaryotes and Prokmentioning

confidence: 93%

Section: The Termination Signal : Stop Codons and The Role Of Flankinmentioning

confidence: 99%

Endless possibilities: translation termination and stop codon recognition

et al. 2001

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“…In a more detailed investigation, stop codon determinants in six prokaryotic and five eukaryotic genomes were studied with the same conclusions (12). In other earlier works, the context of surrounding nucleotides, especially those immediately after the stop codon, in translation termination has been discussed (10,13,14). Also, tools such as TRANSTERM were prepared to investigate the up-and downstream regions of stop codons in a given species (9).…”

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confidence: 99%

Comprehensive Analysis of Stop Codon Usage in Bacteria and Its Correlation with Release Factor Abundance

Korkmaz

Holm

Wiens

et al. 2014

Journal of Biological Chemistry

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Background: Stop codon frequencies in 4684 bacterial genomes are analyzed. Results: With increasing genomic GC content, TAA% decreases, and TGA% increases reciprocally, but TAG% remains almost unchanged (ϳ20%). The TAG:TGA ratio matches well with the RF1:RF2 ratio. Conclusion: TAG is the minor stop codon, and expression of genes with TAG is correlated with the RF1 level. Significance: Our work establishes the correlation between stop codon frequency and RF1/RF2 abundance.

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“…Indeed, in E. coli where the +4 base was altered, each of the three stop codons showed a widely differing hierarchy of termination signal efficiencies dependent on the identity of this base ( Figure 5A). Strength of 4-base signals, UAAN and UGAN, correlated well with the frequency at which they are found at natural termination sites in E. coli [18]. Moreover, if the crosslinking moiety was placed on the +4 base within the designed mRNA, then a crosslink additional to that found from position 1 was obtained, indicating that the decoding RF also made close contact with this base.…”

Section: Is the Decoding Rf More Promiscuous Than A Trna In Its Contamentioning

confidence: 60%

“…Methods [18,19] used for obtaining the novel data discussed here and brief strategies for already published experiments are described in Supplementary Information.…”

Section: Methodsmentioning

confidence: 99%

Accommodating the bacterial decoding release factor as an alien protein among the RNAs at the active site of the ribosome

et al. 2007

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The decoding release factor (RF) triggers termination of protein synthesis by functionally mimicking a tRNA to span the decoding centre and the peptidyl transferase centre (PTC) of the ribosome. Structurally, it must fit into a site crafted for a tRNA and surrounded by five other RNAs, namely the adjacent peptidyl tRNA carrying the completed polypeptide, the mRNA and the three rRNAs. This is achieved by extending a structural domain from the body of the protein that results in a critical conformational change allowing it to contact the PTC. A structural model of the bacterial termination complex with the accommodated RF shows that it makes close contact with the first, second and third bases of the stop codon in the mRNA with two separate loops of structure: the anticodon loop and the loop at the tip of helix a5. The anticodon loop also makes contact with the base following the stop codon that is known to strongly influence termination efficiency. It confirms the close contact of domain 3 of the protein with the key RNA structures of the PTC. The mRNA signal for termination includes sequences upstream as well as downstream of the stop codon, and this may reflect structural restrictions for specific combinations of tRNA and RF to be bound onto the ribosome together. An unbiased SELEX approach has been investigated as a tool to identify potential rRNA-binding contacts of the bacterial RF in its different binding conformations within the active centre of the ribosome.

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The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli.

Cited by 247 publications

References 54 publications

Endless possibilities: translation termination and stop codon recognition

Endless possibilities: translation termination and stop codon recognition

Comprehensive Analysis of Stop Codon Usage in Bacteria and Its Correlation with Release Factor Abundance

Accommodating the bacterial decoding release factor as an alien protein among the RNAs at the active site of the ribosome

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