The 8. The positions of initiation and termination codons are indicated by closed triangles and circles, respectively. The two primary polypeptides of 65 and 80 kDa are indicated by single lines. This polypeptide is subsequently cleaved into the gag protein, a protease of 13 kDa and the reverse transcriptase of kDa. Figure 4. The Figure 5. Figure 6. Figure 7. Nucleotide sequences of cytoplasmic cyt tRNAs Leu from calf liver The modified nucleoside not listed in the Figure 5 legend is m 3 C, 3-methylcytidine.
Figure 8. Figure 9. Figure Nucleotide sequences of cytoplasmic cyt tRNAs Arg from wheat germ. Unconventional base interactions involved in the misreading of termination codons by natural suppressor tRNAs.
A Schematic presentation of putative anticodon—codon interactions by eukaryotic suppressor tRNAs. In the case of the two former examples, incorporation of lysine and tryptophan in addition to tyrosine has been elucidated by amino acid sequence analysis of the translation protein produced by readthrough of an in-frame UAG codon within the yeast Ste6 gene B Hypothetical interactions between non-complementary bases.
In purine—purine mismatches, the nucleoside of the anticodon is presented in the syn configuration isomerisation about the glycosyl bond of the nucleotide. The adenosine in G:A and C:A mismatches is shown in the protonated form. Plant viral readthrough sites. The luteoviruses and PLRV are separated by a horizontal line from the other type III viruses because their stop codons are followed by a valine instead of a glycine codon.
Animal viral readthrough sites. Virus Res. EMBO J. FEBS Lett. Trends Biotechnol. Plant Mol. Microbiology , , — Nucleic Acids Res. Acta , , — Nature , , — Natl Acad. USA , 79 , — Virology , , 18 — USA , 82 , — Virology , , — Nature , , 87 — Plant Sci. USA , 75 , — Gene , 49 , — USA , 84 , — Bacteriol ogy , , — USA , 86 , — Intervirology , 17 , — Evidence that a D-arm mutation reduces tRNA dissociation from the ribosome. Nature , , 41 — USA , 87 , — USA , 88 , — Gene , , — Biochemistry , 37 , — USA , 83 , — Biochimie , 76 , — Cell Biol.
Biochemistry , 27 , — The universal system of virus taxonomy, updated to include the new proposals ratified by the international committee on taxonomy of viruses during Virology , , 92 — Oxford University Press is a department of the University of Oxford. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide. Sign In or Create an Account. Sign In. Advanced Search. Search Menu. Article Navigation.
Close mobile search navigation Article Navigation. Volume Article Contents Abstract. Misreading of termination codons in eukaryotes by natural nonsense suppressor tRNAs. Hildburg Beier , Hildburg Beier. Oxford Academic. Google Scholar. Michael Grimm. Select Format Select format.
Permissions Icon Permissions. Abstract Translational stop codon readthrough provides a regulatory mechanism of gene expression that is extensively utilised by positive-sense ssRNA viruses. Open in new tab Download slide. Issue Section:. Fig 2. Ribosome occupancy over stop codons increases in the absence of RF3 in E.
Release factor expression We also used the ribosome profiling data to examine release factor expression in each strain. Fig 3. Increased rate of programmed frameshifting at the prfB locus. Table 2. Expression of release factors in K and release factor mutants. Fig 4. Fig 5. Schematic explaining ORF classification as recoding or non-recoding. Genes with high post-ORF ribosome occupancy show extended protein products We tested whether our screening criterion, reduced ribosome density after a stop codon in the post-ORF region, identifies genes with a recoding event for three individual genes: nudL and panZ identified in this work, and pheL , a known frameshifter S1 Table [ 50 ].
Fig 6. Coupled genes in polycistronic operons Genes in E. Fig 7. Discussion It is critically important for organisms to terminate the translation of proteins accurately and in an appropriate time frame. Materials and methods Bacterial strains and their construction All experiments were performed in E. Ribosome profiling Ribosome profiling was performed as previously described by Oh et al [ 49 ]. Sequencing analysis Generated sequencing reads were analyzed as previously described [ 46 , 49 ].
Post-ORF region calculations Genome wide calculations of ribosomes in the post-ORF occupancy were performed for all genes with an intergenic region of 65bp or greater that had average mRNA and ribosome footprint densities of 0. Supporting information. S1 Fig. Ribosome occupancy over stop codons. S2 Fig. Increased ribosome occupancy over stop codons of single genes.
S3 Fig. Ribosome occupancy over stop codons of genes with high translation efficiency. S4 Fig. S5 Fig. S6 Fig. Recoding at the pheL locus in all RF mutants. S7 Fig. Western blots of C-terminal tag NudL constructs. S8 Fig. Western blots of NudL and PanZ constructs in all strains. S9 Fig. Translation of overlapping ORF pairs. S10 Fig. S1 Table. Annotated likely recoding events. S2 Table. Annotated possible recoding events.
S3 Table. Annotated non-recoding events. S4 Table. Misannotations resulting in high RPOR values. S5 Table. Stop codon distribution of annotated recoding events. References 1. Zaher HS, Green R. Elsevier Inc. View Article Google Scholar 2. Francklyn CS. View Article Google Scholar 3. Ribosome structure and dynamics during translocation and termination.
Annu Rev Biophys. RF3:GTP promotes rapid dissociation of the class 1 termination factor. Korostelev A a. Structural aspects of translation termination on the ribosome. The accuracy of codon recognition by polypeptide release factors.
Release factor-dependent false stops are infrequent in Escherichia coli. J Mol Biol. The ribosome-recycling step: consensus or controversy? Trends Biochem Sci. J Biol Chem. Hirashima A, Kaji A. Role of elongation factor G and a protein factor on the release of ribosomes from messenger ribonucleic acid.
A single proteolytic cleavage in release factor 2 stabilizes ribosome binding and abolishes peptidyl-tRNA hydrolysis activity. Peptide release on the ribosome: mechanism and implications for translational control. Annu Rev Microbiol. Curr Opin Struct Biol. Elsevier Ltd; ; — View Article Google Scholar Methylation of bacterial release factors RF1 and RF2 is required for normal translation termination in vivo.
Functional specificity of amino acid at position in the tRNA mimicry domain of bacterial release factor 2. A post-translational modification in the GGQ motif of RF2 from Escherichia coli stimulates termination of translation.
EMBO J. Release factor one is nonessential in Escherichia coli. ACS Chem Biol. RF1 knockout allows ribosomal incorporation of unnatural amino acids at multiple sites. Nat Chem Biol. Competition between frameshifting, termination and suppression at the frameshift site in the Escherichia coli release factor-2 mRNA.
Nucleic Acids Res. Expression of peptide chain release factor 2 requires high-efficiency frameshift. Peptide chain termination: effect of protein S on ribosomal binding of release factors. Release factor RF3 in E. Visualization of release factor 3 on the ribosome during termination of protein synthesis. Mol Microbiol. Mol Cell. Sequence and functional analysis of mutations in the gene encoding peptide-chain-release factor 2 of Escherichia coli.
Elliott T, Wang X. J Bacteriol. Kawakami K, Nakamura Y. Autogenous suppression of an opal mutation in the gene encoding peptide chain release factor 2. Identification of the prfC gene, which encodes peptide-chain-release factor 3 of Escherichia coli.
A primary role for release factor 3 in quality control during translation elongation in Escherichia coli. Interactions of release factor RF3 with the translation machinery. Mol Genet Genomics. Conditionally lethal and recessive UGA-suppressor mutations in the prfB gene encoding peptide chain release factor 2 of Escherichia coli.
Suppression of temperature-sensitive defects of polypeptide release factors RF-1 and RF-2 by mutations or by an excess of RF-3 in Escherichia coli. Indirect regulation of translational termination efficiency at highly expressed genes and recoding sites by the factor recycling function of Escherichia coli release factor RF3.
Distinct roles for release factor 1 and release factor 2 in translational quality control. Localization and characterization of the gene encoding release factor RF3 in Escherichia coli.
Phenotypic landscape of a bacterial cell. Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Elsevier; ; — The identity of the base following the stop codon determines the efficiency of in vivo translational termination in Escherichia coli.
Comparative study of translation termination sites and release factors RF1 and RF2 in procaryotes. J Mol Evol. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.
Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. High sequence specificity of micrococcal nuclease. Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo. Gurvich O, Baranov P. Sequences that direct significant levels of frameshifting are frequent in coding regions of Escherichia coli. Two groups of phenylalanine biosynthetic operon leader peptides genes: a high level of apparently incidental frameshifting in decoding Escherichia coli pheL.
Huvet M, Stumpf MP. Overlapping genes: a window on gene evolvability. BMC Genomics. Translational coupling of the trpB and trpA genes in the Escherichia coli Tryptophan operon. Oppenheim DS, Yanofsky C. Translational coupling during expression of the tryptophan operon of Escherichia coli.
Translational coupling at an intercistronic boundary of the Escherichia coli galactose operon. Yates JL, Nomura M. Feedback regulation of ribosomal protein synthesis in E. Yanofsky C. The translational stop signal: Codon with a context, or extended factor recognition element? A posttermination ribosomal complex is the guanine nucleotide exchange factor for peptide release factor RF3.
Consequently, a new selective regime imposed by codon reassignment would also make a contribution to the evolutionary success or failure of an organism as a consequence of the effects on fitness arising from changes in gene length.
Further work, especially experimental work, will be necessary in order to disentangle cause from effect - note that if codon reassignment and proteome length influence one another, each can be both cause and effect - and to establish the most likely sequence of events involved in stop codon reassignment.
Unfortunately, without values for R , which in any case is likely to vary between genes, and k , our model - which, like all such models, presents a greatly simplified picture of an extremely complex process - does not allow us predict the optimal number of stop codons in a particular genome.
It might be possible to get some indication of plausible values for R from, for instance, the number of amino acids that can be added to a protein's C-terminus during purification without affecting its conformation and activity, but since R will also vary with the precise downstream sequence for example, extremely hydrophobic residues might have a greater impact even this is likely to be largely uninformative.
Despite this, our model does allow us to make predictions, such as those tested here, about broad patterns relating to the length of the coding sequence.
For each of the protein-coding transcripts annotated in build 36, version 3 of the NCBI RefSeq of the human genome, the coding sequence plus bp immediately downstream of the terminal stop were extracted. Each of these sequences was randomly reordered times thus preserving GC content and base composition ratios for each , and for downstream sequence, the position of the first in-frame stop was calculated and compared to the position in the actual data.
For both the actual and randomised sequence, where there was no downstream stop in this bp sequence, its position was taken to be at the th triplet.
The distributions of downstream stop positions in the actual data and in the randomisations were compared using a Kolmogorov-Smirnov test. The same figures were also calculated taking just a single transcript for each of the 22, protein-coding genes, with essentially identical results, the average difference per data point between the two approaches being 0. Scripts used in the analysis are available on request from the authors. In all cases, the taxon name in the Organism field was required.
For bacteria and mitochondria, only fully sequenced genomes were compared. For eukaryotic nuclear genes, "mitochondrial", "mitochondrion" and "chloroplast" were also excluded; "complete" was required to exclude single exons and partial coding sequences. This criterion also excluded many coding sequences from whole genome sequencing projects, avoiding a comparison between fully sequenced and unsequenced genomes which are likely to differ in genes surveyed.
For mitochondrial datasets excepting Euglenozoa and Haptophyta, "complete genome" plus "mitochondrion" or "mitochondrial" in the title were required. In the Euglenozoa and Haptophyta no fully sequenced mitochondrial genome comparisons were possible; in these cases complete mitochondrial gene sequences were downloaded. A Perl script then extracted coding sequence co-ordinates, calculated protein length, and attributed lengths to particular genetic codes according to the translation table ascribed in GenBank.
Perl scripts and datasets are available on request from the authors. Article Google Scholar. J Thromb Haem. Nature Rev Mol Cell Biol. Bonetti B, Fu L, Moon J, Bedwell DM: The efficiency of translation termination is determined by a synergistic interplay between upstream and downstream sequences in Saccharomyces cerevisiae.
J Mol Biol. Genome Biology. J Mol Evol. FEBS Letters. Eyre-Walker A: The close proximity of Escherichia coli genes: consequences for stop codon and synonymous codon use. Phil Trans Roy Soc. Ann Rev Genet. Kotlar D, Lavner Y: The action of selection of codon bias in the human genome is related to frequency, complexity, and chronology of amino acids.
BMC Genomics. PLoS Genet. Nature Rev Genetics. Itzkovitz S, Alon U: The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res. DNA and Cell Biol. PLoS Biol. Microbiol Rev. Comp Biochem Physiol. CAS Google Scholar. Download references. You can also search for this author in PubMed Google Scholar.
Correspondence to Steven C Le Comber. CPL co-conceived the project. All authors read and approved the final manuscript. Additional File Table S1 details genetic codes, numbers of coding sequences available, mean gene length, and significance of differences in mean gene length, for each taxon shown in Figure 2. DOC 86 KB. Reprints and Permissions. Johnson, L.
Stops making sense: translational trade-offs and stop codon reassignment. BMC Evol Biol 11, Download citation. Received : 20 December Accepted : 29 July Published : 29 July Anyone you share the following link with will be able to read this content:.
Sorry, a shareable link is not currently available for this article. Provided by the Springer Nature SharedIt content-sharing initiative.
Skip to main content. Search all BMC articles Search. Download PDF. Abstract Background Efficient gene expression involves a trade-off between i premature termination of protein synthesis; and ii readthrough, where the ribosome fails to dissociate at the terminal stop. Results In the human genome, codons readily mutable to stops are underrepresented in coding sequences.
Conclusions We suggest that the differing trade-offs presented by alternative genetic codes may result in differences in genome structure. Background Premature termination of protein synthesis is costly, whether it is caused by heritable mutation, transcriptional error or mistranslation.
0コメント