Genomes and Genes
Summary: Any codon that signals the termination of genetic translation (TRANSLATION, GENETIC). PEPTIDE TERMINATION FACTORS bind to the stop codon and trigger the hydrolysis of the aminoacyl bond connecting the completed polypeptide to the tRNA. Terminator codons do not specify amino acids.
- Hirosawa Takamori M, Ossipov D, Novoselov S, Turanov A, Zhang Y, Gladyshev V, et al. A novel stem loop control element-dependent UGA read-through system without translational selenocysteine incorporation in Drosophila. FASEB J. 2009;23:107-13 pubmed publisher..The results indicate that GAPsec is part of a novel SECIS-dependent translational read-through system that does not involve selenocysteine incorporation. ..
- Pallejà A, Harrington E, Bork P. Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions?. BMC Genomics. 2008;9:335 pubmed publisher..We propose a simple rule to flag these erroneous gene length predictions to facilitate automatic annotation. ..
- Stoytcheva Z, Tujebajeva R, Harney J, Berry M. Efficient incorporation of multiple selenocysteines involves an inefficient decoding step serving as a potential translational checkpoint and ribosome bottleneck. Mol Cell Biol. 2006;26:9177-84 pubmed..The implications for how these factors contribute to the decoding of multiple selenocysteine residues are discussed. ..
- Pöyry T, Kaminski A, Connell E, Fraser C, Jackson R. The mechanism of an exceptional case of reinitiation after translation of a long ORF reveals why such events do not generally occur in mammalian mRNA translation. Genes Dev. 2007;21:3149-62 pubmed
- Squires J, Berry M. Eukaryotic selenoprotein synthesis: mechanistic insight incorporating new factors and new functions for old factors. IUBMB Life. 2008;60:232-5 pubmed publisher..Herein, we discuss the various proteins known to function in eukaryotic selenoprotein biosynthesis, including several players whose roles have only been elucidated very recently. ..
- Fan Minogue H, Du M, Pisarev A, Kallmeyer A, Salas Marco J, Keeling K, et al. Distinct eRF3 requirements suggest alternate eRF1 conformations mediate peptide release during eukaryotic translation termination. Mol Cell. 2008;30:599-609 pubmed publisher..These results suggest that the TASNIKS motif and eRF3 function together to trigger eRF1 conformational changes that couple stop codon recognition and peptide release during eukaryotic translation termination...
- Singh T, Pardasani K. Ambush hypothesis revisited: Evidences for phylogenetic trends. Comput Biol Chem. 2009;33:239-44 pubmed publisher..Strongest impact of this event was found in viruses and bacteria. It has been suggested that this mechanism has occurred and been utilized in the early stages of evolution. ..
- von der Haar T, Tuite M. Regulated translational bypass of stop codons in yeast. Trends Microbiol. 2007;15:78-86 pubmed..Rather than being a translation 'error', stop-codon readthrough can have important effects on other cellular processes such as mRNA degradation and, in some cases, can confer a beneficial phenotype to the cell. ..
- Itzkovitz S, Alon U. The genetic code is nearly optimal for allowing additional information within protein-coding sequences. Genome Res. 2007;17:405-12 pubmed..Whereas many of the known regulatory codes reside in nontranslated regions of the genome, the present findings suggest that protein-coding regions can readily carry abundant additional information. ..
- Slamovits C, Saldarriaga J, Larocque A, Keeling P. The highly reduced and fragmented mitochondrial genome of the early-branching dinoflagellate Oxyrrhis marina shares characteristics with both apicomplexan and dinoflagellate mitochondrial genomes. J Mol Biol. 2007;372:356-68 pubmed..Overall, the combination of characteristics found in the Oxyrrhis genome allows us to plot the sequence of many events that led to the extreme organisation of apicomplexan and dinoflalgellate mitochondrial genomes. ..
- Raczynska K, Le Ret M, Rurek M, Bonnard G, Augustyniak H, Gualberto J. Plant mitochondrial genes can be expressed from mRNAs lacking stop codons. FEBS Lett. 2006;580:5641-6 pubmed..Using antibodies directed against CcmC, the corresponding protein was detected in Arabidopsis mitochondrial extracts. These observations raise the question of how the plant mitochondrial translation system deals with non-stop mRNAs. ..
- Wong T, Fernandes S, Sankhon N, Leong P, Kuo J, Liu J. Role of premature stop codons in bacterial evolution. J Bacteriol. 2008;190:6718-25 pubmed publisher..We proposed that the quantity and the quality of the PSC in the genome might be important in bacterial evolution. ..
- Sengupta S, Yang X, Higgs P. The mechanisms of codon reassignments in mitochondrial genetic codes. J Mol Evol. 2007;64:662-88 pubmed..We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully. ..
- Powell M, Napthine S, Jackson R, Brierley I, Brown T. Characterization of the termination-reinitiation strategy employed in the expression of influenza B virus BM2 protein. RNA. 2008;14:2394-406 pubmed publisher..This suggests that the full complement of initiation factors is not required for the reinitiation process. ..
- Mora L, Heurgué Hamard V, de Zamaroczy M, Kervestin S, Buckingham R. Methylation of bacterial release factors RF1 and RF2 is required for normal translation termination in vivo. J Biol Chem. 2007;282:35638-45 pubmed..This suggests that the expression of some genes needed for optimal growth under such conditions can become growth limiting as a result of inefficient translation termination. ..
- Gupta M, Copeland P. Functional analysis of the interplay between translation termination, selenocysteine codon context, and selenocysteine insertion sequence-binding protein 2. J Biol Chem. 2007;282:36797-807 pubmed..We conclude that a large codon context forms a cis-element that works together with Sec incorporation factors to determine readthrough efficiency. ..
- Chapple C, Guigo R, Krol A. SECISaln, a web-based tool for the creation of structure-based alignments of eukaryotic SECIS elements. Bioinformatics. 2009;25:674-5 pubmed publisher..SECISaln is freely available as a web-based tool at http://genome.crg.es/software/secisaln/. ..
- Laurberg M, Asahara H, Korostelev A, Zhu J, Trakhanov S, Noller H. Structural basis for translation termination on the 70S ribosome. Nature. 2008;454:852-7 pubmed publisher..Unexpectedly, the main-chain amide group of Gln 230 in the universally conserved GGQ motif of the factor is positioned to contribute directly to peptidyl-tRNA hydrolysis. ..
- Amrani N, Sachs M, Jacobson A. Early nonsense: mRNA decay solves a translational problem. Nat Rev Mol Cell Biol. 2006;7:415-25 pubmed..New evidence indicates that the specialized factors that are recruited for this process not only promote rapid mRNA degradation, but are also required to resolve a poorly dissociable termination complex. ..
- Kononenko A, Mitkevich V, Dubovaya V, Kolosov P, Makarov A, Kisselev L. Role of the individual domains of translation termination factor eRF1 in GTP binding to eRF3. Proteins. 2008;70:388-93 pubmed
- Boore J. The complete sequence of the mitochondrial genome of Nautilus macromphalus (Mollusca: Cephalopoda). BMC Genomics. 2006;7:182 pubmed publisher..tunicata implies that mutational bias during replication also plays a role. This appears to be yet another case where polyadenylation of mitochondrial tRNAs restores what would otherwise be an incomplete structure...
- Alkalaeva E, Eliseev B, Ambrogelly A, Vlasov P, Kondrashov F, Gundllapalli S, et al. Translation termination in pyrrolysine-utilizing archaea. FEBS Lett. 2009;583:3455-60 pubmed publisher..The second aRF1 homolog may have another unknown function. The mechanism of pyrrolysine incorporation in the Methanosarcinaceae is discussed. ..
- Khajavi M, Inoue K, Lupski J. Nonsense-mediated mRNA decay modulates clinical outcome of genetic disease. Eur J Hum Genet. 2006;14:1074-81 pubmed..Here, we review the physiological role of this surveillance pathway, its implications for human diseases, and why knowledge of NMD is important to an understanding of genotype-phenotype correlations in various genetic disorders. ..
- Alkalaeva E, Pisarev A, Frolova L, Kisselev L, Pestova T. In vitro reconstitution of eukaryotic translation reveals cooperativity between release factors eRF1 and eRF3. Cell. 2006;125:1125-36 pubmed..Cooperativity between eRF1 and eRF3 required the eRF3 binding C-terminal domain of eRF1. ..
- Petry S, Brodersen D, Murphy F, Dunham C, Selmer M, Tarry M, et al. Crystal structures of the ribosome in complex with release factors RF1 and RF2 bound to a cognate stop codon. Cell. 2005;123:1255-66 pubmed publisher..Finally, this work demonstrates the feasibility of crystallizing ribosomes with bound factors at a defined state along the translational pathway...
- Dreher T, Miller W. Translational control in positive strand RNA plant viruses. Virology. 2006;344:185-97 pubmed..Finally, future directions for research on the translation of plant positive strand viruses are discussed. ..
- Chaudhuri B, Yeates T. A computational method to predict genetically encoded rare amino acids in proteins. Genome Biol. 2005;6:R79 pubmed..A survey across a set of microbial genomes identifies almost all the known cases as well as a number of novel candidate proteins. ..
- Oparina N, Kalinina O, Gelfand M, Kisselev L. Common and specific amino acid residues in the prokaryotic polypeptide release factors RF1 and RF2: possible functional implications. Nucleic Acids Res. 2005;33:5226-34 pubmed..Presumably, they also take part in stop codon binding and discrimination. Elucidation of potential functional role(s) of the newly identified SDP/IR zones requires further experiments. ..
- Liu Q. Comparative analysis of base biases around the stop codons in six eukaryotes. Biosystems. 2005;81:281-9 pubmed..Accordingly, it could be inferred that those candidate amino acids might involve in the recognition process. Moreover, the possible stop signal recognition hypothesis was also discussed herein. ..
- Cochella L, Green R. An active role for tRNA in decoding beyond codon:anticodon pairing. Science. 2005;308:1178-80 pubmed..These data provide evidence for a direct role for tRNA in signaling its own acceptance during decoding and support its fundamental role during the evolution of protein synthesis. ..
- Liang H, Wong J, Bao Q, Cavalcanti A, Landweber L. Decoding the decoding region: analysis of eukaryotic release factor (eRF1) stop codon-binding residues. J Mol Evol. 2005;60:337-44 pubmed..Our results are more consistent with current experimental data than previously described models. ..
- Salas Marco J, Bedwell D. Discrimination between defects in elongation fidelity and termination efficiency provides mechanistic insights into translational readthrough. J Mol Biol. 2005;348:801-15 pubmed..We used this misincorporation reporter in conjunction with a readthrough reporter system to show that alterations at different regions of the ribosome influence elongation fidelity and termination efficiency to different extents. ..
- Chavatte L, Brown B, Driscoll D. Ribosomal protein L30 is a component of the UGA-selenocysteine recoding machinery in eukaryotes. Nat Struct Mol Biol. 2005;12:408-16 pubmed..We propose a model in which SBP2 and L30 carry out different functions in the UGA recoding mechanism, with the SECIS acting as a molecular switch upon protein binding. ..
- Kim O, Yura K, Go N, Harumoto T. Newly sequenced eRF1s from ciliates: the diversity of stop codon usage and the molecular surfaces that are important for stop codon interactions. Gene. 2005;346:277-86 pubmed..Using computational methods, we have also suggested areas on the surface of eRF1s that are important for stop codon recognition in ciliate eRF1s. ..
- Cobucci Ponzano B, Rossi M, Moracci M. Recoding in archaea. Mol Microbiol. 2005;55:339-48 pubmed..Therefore, it appears that the study of this phenomenon in Archaea is still at its dawn and that most of the genes whose expression is regulated by recoding are still uncharacterized. ..
- Seligmann H, Pollock D. The ambush hypothesis: hidden stop codons prevent off-frame gene reading. DNA Cell Biol. 2004;23:701-5 pubmed..Some experimental data confirm our hypothesis: gene expression increases with the experimentally manipulated number of stops in the promoter region of a gene, suggesting biotechnological applications. ..
- Perrodou E, Deshayes C, Muller J, Schaeffer C, Van Dorsselaer A, Ripp R, et al. ICDS database: interrupted CoDing sequences in prokaryotic genomes. Nucleic Acids Res. 2006;34:D338-43 pubmed..This allows us to estimate the specificity and sensitivity (95 and 82%, respectively) of our program and the efficiency of primer determination. ..
- Kolosov P, Frolova L, Seit Nebi A, Dubovaya V, Kononenko A, Oparina N, et al. Invariant amino acids essential for decoding function of polypeptide release factor eRF1. Nucleic Acids Res. 2005;33:6418-25 pubmed..The data point to a pivotal role played by the YxCxxxF motif (positions 125-131) in purine discrimination of the stop codons. We speculate that eRF1 decoding site is formed by a 3D network of amino acids side chains. ..
- Kojima K, Matsumoto T, Fujiwara H. Eukaryotic translational coupling in UAAUG stop-start codons for the bicistronic RNA translation of the non-long terminal repeat retrotransposon SART1. Mol Cell Biol. 2005;25:7675-86 pubmed..The translational mechanism of SART1 ORF2 is analogous to translational coupling observed in prokaryotes and viruses. Our results indicate that translational coupling is a general mechanism for bicistronic RNA translation. ..
- Rospert S, Rakwalska M, Dubaquie Y. Polypeptide chain termination and stop codon readthrough on eukaryotic ribosomes. Rev Physiol Biochem Pharmacol. 2005;155:1-30 pubmed..This review explores our current understanding of eukaryotic termination by highlighting the roles of the different ribosomal components as well as termination factors and ribosome-associated proteins, such as chaperones. ..
- Zhang Y, Baranov P, Atkins J, Gladyshev V. Pyrrolysine and selenocysteine use dissimilar decoding strategies. J Biol Chem. 2005;280:20740-51 pubmed..Thus, Sec and Pyl follow dissimilar decoding and evolutionary strategies. ..
- Williams I, Richardson J, Starkey A, Stansfield I. Genome-wide prediction of stop codon readthrough during translation in the yeast Saccharomyces cerevisiae. Nucleic Acids Res. 2004;32:6605-16 pubmed..The approaches described can be employed to define potential readthrough contexts for any genome. ..
- Howard M, Malik N, Anderson C, Voskuil J, Atkins J, Gibbons R. Attenuation of an amino-terminal premature stop codon mutation in the ATRX gene by an alternative mode of translational initiation. J Med Genet. 2004;41:951-6 pubmed
- Liu Q, Xue Q. Computational identification and sequence analysis of stop codon readthrough genes in Oryza sativa. Biosystems. 2004;77:33-9 pubmed..7%), which indicated that the amino acids at the readthrough region being frequently located in the hydrophilic region of beta-turn might be a determinant for efficient translation termination or not. ..
- Rios J, Perelygin A, Long M, Lear T, Zharkikh A, Brinton M, et al. Characterization of the equine 2'-5' oligoadenylate synthetase 1 (OAS1) and ribonuclease L (RNASEL) innate immunity genes. BMC Genomics. 2007;8:313 pubmed publisher..These polymorphisms are the first to be reported for these genes and will facilitate future case-control studies of horse susceptibility to infectious diseases...
- Yu J, Pon C, Ku H, Wang C, Kao Y. A preprogalanin cDNA from the turtle pituitary and regulation of its gene expression. Am J Physiol Regul Integr Comp Physiol. 2007;292:R1649-56 pubmed..These results suggest a hormone-dependent effect on hypophyseal galanin mRNA expression. ..
- Kofuji S, Sakuno T, Takahashi S, Araki Y, Doi Y, Hoshino S, et al. The decapping enzyme Dcp1 participates in translation termination through its interaction with the release factor eRF3 in budding yeast. Biochem Biophys Res Commun. 2006;344:547-53 pubmed..These results suggest that the decapping enzyme Dcp1p may have an additional role in the translation termination through its interaction with eRF3p. ..
- Mitra A, Angamuthu K, Jayashree H, Nagaraja V. Occurrence, divergence and evolution of intrinsic terminators across eubacteria. Genomics. 2009;94:110-6 pubmed publisher..The software and detailed results for individual genomes are freely available on request. ..
- Pankhong P, Weiner D, Ramanathan M, Nisalak A, Kalayanarooj S, Nimmannitya S, et al. Molecular genetic relationship of the 3' untranslated region among Thai dengue-3 virus, Bangkok isolates, during 1973-2000. DNA Cell Biol. 2009;28:481-91 pubmed publisher..Correlation with disease severity suggests that both primary sequences and secondary structures of the 3' UTR do not appear correlated with disease severity in humans. ..
- Dunkle J, Cate J. Ribosome structure and dynamics during translocation and termination. Annu Rev Biophys. 2010;39:227-44 pubmed publisher..Finally, we review recent advances in understanding how bacteria handle errors in both translocation and termination. ..
- Chemin G, Tinguely A, Sirac C, Lechouane F, Duchez S, Cogne M, et al. Multiple RNA surveillance mechanisms cooperate to reduce the amount of nonfunctional Ig kappa transcripts. J Immunol. 2010;184:5009-17 pubmed publisher..Altogether, these data show that nonfunctionally rearranged alleles are subjected to active transcription but that multiple RNA surveillance mechanisms eradicate up to 90% of out-of-frame Igkappa mRNA. ..