codon

Summary

Summary: A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).

Top Publications

  1. Ni Y, Zhao Z, Opriessnig T, Subramaniam S, Zhou L, Cao D, et al. Computer-aided codon-pairs deoptimization of the major envelope GP5 gene attenuates porcine reproductive and respiratory syndrome virus. Virology. 2014;450-451:132-9 pubmed publisher
    ..The major envelope GP5 gene of PRRSV was codon-pair deoptimized aided by a computer algorithm...
  2. Jackson W, Borkowski A, Watson N, King O, Faas H, Jasanoff A, et al. Profoundly different prion diseases in knock-in mice carrying single PrP codon substitutions associated with human diseases. Proc Natl Acad Sci U S A. 2013;110:14759-64 pubmed publisher
    ..We conclude that single codon differences in a single gene in an otherwise normal genome can cause remarkably different neurodegenerative ..
  3. Krishnakumar R, Prat L, Aerni H, Ling J, Merryman C, Glass J, et al. Transfer RNA misidentification scrambles sense codon recoding. Chembiochem. 2013;14:1967-72 pubmed publisher
    Sense codon recoding is the basis for genetic code expansion with more than two different noncanonical amino acids...
  4. Roller M, Lucić V, Nagy I, Perica T, Vlahovicek K. Environmental shaping of codon usage and functional adaptation across microbial communities. Nucleic Acids Res. 2013;41:8842-52 pubmed publisher
    ..By exploring concepts of translational optimization through codon usage adaptation, we demonstrated that community-wide bias in codon usage can be used as a prediction tool for ..
  5. Park J, Ao L, Miller Z, Kim K, Wu Y, Jang E, et al. PSMB9 codon 60 polymorphisms have no impact on the activity of the immunoproteasome catalytic subunit B1i expressed in multiple types of solid cancer. PLoS ONE. 2013;8:e73732 pubmed publisher
    ..In particular, the codon 60 polymorphism of the PSMB9 gene encoding the ?1i immunoproteasome catalytic subunit has been investigated in the ..
  6. Colson P, Fournous G, Diene S, Raoult D. Codon usage, amino acid usage, transfer RNA and amino-acyl-tRNA synthetases in Mimiviruses. Intervirology. 2013;56:364-75 pubmed publisher
    ..We analyzed the codon and amino acid usages in mimiviruses, as well as both the transfer RNA (tRNA) and amino acyl-tRNA synthetases...
  7. Chen Y. A comparison of synonymous codon usage bias patterns in DNA and RNA virus genomes: quantifying the relative importance of mutational pressure and natural selection. Biomed Res Int. 2013;2013:406342 pubmed publisher
    b>Codon usage bias patterns have been broadly explored for many viruses. However, the relative importance of mutation pressure and natural selection is still under debate...
  8. Zhou J, Zhang J, Sun D, Ma Q, Chen H, Ma L, et al. The distribution of synonymous codon choice in the translation initiation region of dengue virus. PLoS ONE. 2013;8:e77239 pubmed publisher
    Dengue is the most common arthropod-borne viral (Arboviral) illness in humans. The genetic features concerning the codon usage of dengue virus (DENV) were analyzed by the relative synonymous codon usage, the effective number of codons ..
  9. Kogure H, Handa Y, Nagata M, Kanai N, Güntert P, Kubota K, et al. Identification of residues required for stalled-ribosome rescue in the codon-independent release factor YaeJ. Nucleic Acids Res. 2014;42:3152-63 pubmed publisher
    The YaeJ protein is a codon-independent release factor with peptidyl-tRNA hydrolysis (PTH) activity, and functions as a stalled-ribosome rescue factor in Escherichia coli...

More Information

Publications62

  1. Karsy M, Albert L, Murali R, Jhanwar Uniyal M. The impact of arsenic trioxide and all-trans retinoic acid on p53 R273H-codon mutant glioblastoma. Tumour Biol. 2014;35:4567-80 pubmed publisher
    Glioblastoma (GBM) is the most common primary brain tumor in adults and demonstrates a 1-year median survival time. Codon-specific hotspot mutations of p53 result in constitutively active mutant p53, which promotes aberrant proliferation,..
  2. Hirschmann W, Westendorf H, Mayer A, Cannarozzi G, Cramer P, Jansen R. Scp160p is required for translational efficiency of codon-optimized mRNAs in yeast. Nucleic Acids Res. 2014;42:4043-55 pubmed publisher
    ..Our data indicate that Scp160p might increase the efficiency of tRNA recharge, or prevent diffusion of discharged tRNAs, both of which were also proposed to be the likely basis for the translational fitness effect of tRNA pairing...
  3. Stergachis A, Haugen E, Shafer A, Fu W, Vernot B, Reynolds A, et al. Exonic transcription factor binding directs codon choice and affects protein evolution. Science. 2013;342:1367-72 pubmed publisher
    ..are highly conserved and have shaped protein evolution, and TF-imposed constraint appears to be a major driver of codon usage bias. Conversely, the regulatory code has been selectively depleted of TFs that recognize stop codons...
  4. Suarez Calvet M, Belbin O, Pera M, Badiola N, Magrane J, Guardia Laguarta C, et al. Autosomal-dominant Alzheimer's disease mutations at the same codon of amyloid precursor protein differentially alter A? production. J Neurochem. 2014;128:330-9 pubmed publisher
    ..However, the differential effect of mutations at the same codon has not been sufficiently addressed...
  5. Er T, Chen C, Bujanda L, Herreros Villanueva M. Clinical relevance of KRAS mutations in codon 13: Where are we?. Cancer Lett. 2014;343:1-5 pubmed publisher
    ..KRAS mutations in codon 12 and 13 are recognized biomarkers that are analyzed in clinic previously for anti-EGFR therapies administration...
  6. Pavesi A, Magiorkinis G, Karlin D. Viral proteins originated de novo by overprinting can be identified by codon usage: application to the "gene nursery" of Deltaretroviruses. PLoS Comput Biol. 2013;9:e1003162 pubmed publisher
    ..set of overlapping genes for which we could reliably determine the ancestral frames, and found that their codon usage was significantly closer to that of the rest of the viral genome than the codon usage of de novo frames...
  7. Trotta E. Selection on codon bias in yeast: a transcriptional hypothesis. Nucleic Acids Res. 2013;41:9382-95 pubmed publisher
    Codons that code for the same amino acid are often used with unequal frequencies. This phenomenon is termed codon bias. Here, we report a computational analysis of codon bias in yeast using experimental and theoretical genome-wide data...
  8. Lauring A, Acevedo A, Cooper S, Andino R. Codon usage determines the mutational robustness, evolutionary capacity, and virulence of an RNA virus. Cell Host Microbe. 2012;12:623-32 pubmed publisher
    ..Because several codon choices are available for a given amino acid, a central question concerns whether viral sequences have evolved to ..
  9. Lazrak A, Fu L, Bali V, Bartoszewski R, Rab A, Havasi V, et al. The silent codon change I507-ATC->ATT contributes to the severity of the ?F508 CFTR channel dysfunction. FASEB J. 2013;27:4630-45 pubmed publisher
    ..This mutation leads to the loss of phenylalanine-508 (?F508) and a silent codon change (SCC) for isoleucine-507 (I507-ATC?ATT)...
  10. Klumpp S, Dong J, Hwa T. On ribosome load, codon bias and protein abundance. PLoS ONE. 2012;7:e48542 pubmed publisher
    ..highly expressed proteins, but a recent study of synthetic GFP-coding sequences did not find a correlation between codon usage and GFP expression, suggesting that such correlation in natural sequences is not a simple property of ..
  11. Bauer F, Hermand D. A coordinated codon-dependent regulation of translation by Elongator. Cell Cycle. 2012;11:4524-9 pubmed publisher
    ..Our recent proteome-wide study in fission yeast supports a coordinated codon-dependent regulation of translation by Elongator...
  12. Yokobori S, Kitamura A, Grosjean H, Bessho Y. Life without tRNAArg-adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes. Nucleic Acids Res. 2013;41:6531-43 pubmed publisher
    ..CGU, CGC and CGA codons, whereas a second tRNA harboring a wobble cytidine (tRNA(Arg)CCG) reads the remaining CGG codon. The reduced genomes of Mycoplasmas and other Mollicutes lack the gene encoding tRNA(Arg)CCG...
  13. Firnberg E, Ostermeier M. PFunkel: efficient, expansive, user-defined mutagenesis. PLoS ONE. 2012;7:e52031 pubmed publisher
    ..We also employ PFunkel to create a comprehensive codon mutagenesis library of the TEM-1 ß-lactamase gene...
  14. Belalov I, Lukashev A. Causes and implications of codon usage bias in RNA viruses. PLoS ONE. 2013;8:e56642 pubmed publisher
    ..were developed to account for these features and analyze the relative impact of mutational pressure components on codon usage bias in RNA viruses...
  15. van der Kuyl A, Berkhout B. The biased nucleotide composition of the HIV genome: a constant factor in a highly variable virus. Retrovirology. 2012;9:92 pubmed publisher
  16. Bouquet J, Cherel P, Pavio N. Genetic characterization and codon usage bias of full-length Hepatitis E virus sequences shed new lights on genotypic distribution, host restriction and genome evolution. Infect Genet Evol. 2012;12:1842-53 pubmed publisher
    ..Nucleotide composition and codon usage bias were determined to characterize HEV host restriction and genome evolution...
  17. Bauer F, Matsuyama A, Candiracci J, Dieu M, Scheliga J, Wolf D, et al. Translational control of cell division by Elongator. Cell Rep. 2012;1:424-33 pubmed
    ..is a central regulator of mitosis and cytokinesis, is under translational control by Elongator due to the Lysine codon usage bias of the cdr2 coding sequence...
  18. Park S, Chang K, Jin E, Pack S, Lee J. Oxaloacetate and malate production in engineered Escherichia coli by expression of codon-optimized phosphoenolpyruvate carboxylase2 gene from Dunaliella salina. Bioprocess Biosyst Eng. 2013;36:127-31 pubmed publisher
    ..Recombinant E. coli SGJS115 with increased production of malate and oxaloacetate was developed by introducing codon-optimized phosphoenolpyruvate carboxylase2 (OPDSPEPC2) gene of Dunaliella salina. E. coli SGJS115 yielded a 9...
  19. Demeshkina N, Jenner L, Westhof E, Yusupov M, Yusupova G. A new understanding of the decoding principle on the ribosome. Nature. 2012;484:256-9 pubmed publisher
    ..factor Tu, which delivers tRNA to the aminoacyl tRNA-binding site (A site) and hydrolyses GTP upon establishing codon-anticodon interactions in the decoding centre...
  20. Zhou Y, Zhou Y, He F, Song J, Zhang Z. Can simple codon pair usage predict protein-protein interaction?. Mol Biosyst. 2012;8:1396-404 pubmed publisher
    ..Here we analyze the relationship between codon pair usage and PPIs in yeast...
  21. Deutsch C, El Yacoubi B, De Crecy Lagard V, Iwata Reuyl D. Biosynthesis of threonylcarbamoyl adenosine (t6A), a universal tRNA nucleoside. J Biol Chem. 2012;287:13666-73 pubmed publisher
    ..The anticodon stem-loop (ASL) of transfer RNAs (tRNAs) drives decoding by interacting directly with the mRNA through codon/anticodon pairing...
  22. Lukashev A, Drexler J, Belalov I, Eschbach Bludau M, Baumgarte S, Drosten C. Genetic variation and recombination in Aichi virus. J Gen Virol. 2012;93:1226-35 pubmed publisher
    ..AiV genomes also appeared to contain a codon usage bias (CUB) apparent as an effective number of codons of 39...
  23. Croteau S, Luo H, Lehmann L, Chui D, Neufeld E. Novel dominant ?-thalassemia: Hb Boston-Kuwait [codon 139/140(+T)]. Pediatr Blood Cancer. 2013;60:E131-4 pubmed publisher
    ..Hematopoietic stem cell transplant provided a successful alternative therapy for this severe form of dominant ?-thalassemia. ..
  24. Lind P, Andersson D. Fitness costs of synonymous mutations in the rpsT gene can be compensated by restoring mRNA base pairing. PLoS ONE. 2013;8:e63373 pubmed publisher
    ..These results suggest that for ribosomal protein S20, the deleterious effects of synonymous mutations are not generally due to codon usage effects, but that mRNA secondary structure is a major fitness constraint.
  25. Xie T, Zhou G, Zhao M, Sano D, Jasser S, Brennan R, et al. Serine substitution of proline at codon 151 of TP53 confers gain of function activity leading to anoikis resistance and tumor progression of head and neck cancer cells. Laryngoscope. 2013;123:1416-23 pubmed publisher
    ..of this study is to determine the gain of function of mutant p53 with a proline-to-serine substitution at codon 151. Laboratory-based study...
  26. Li Y, Kim O, Ito K, Saito K, Suzaki T, Harumoto T. A single amino acid substitution alters omnipotent eRF1 of Dileptus to euplotes-type dualpotent eRF1: standard codon usage may be advantageous in raptorial ciliates. Protist. 2013;164:440-9 pubmed publisher
    ..studies have suggested that the tip region NIKS and its adjacent YxCxxxF motifs in domain 1 are important for stop codon recognition. Litostomatea is a class of ciliate that appears to use the standard genetic code...
  27. Alvarez Dominguez J, Amosova O, Fresco J. Self-catalytic DNA depurination underlies human ?-globin gene mutations at codon 6 that cause anemias and thalassemias. J Biol Chem. 2013;288:11581-9 pubmed publisher
    The human ?-globin gene contains an 18-nucleotide coding strand sequence centered at codon 6 and capable of forming a stem-loop structure that can self-catalyze depurination of the 5'G residue of that codon...
  28. Zhou X, Gu Y, Zhang S. Association between p53 codon 72 polymorphism and cervical cancer risk among Asians: a HuGE review and meta-analysis. Asian Pac J Cancer Prev. 2012;13:4909-14 pubmed
    ..HuGE) review and meta-analysis was to derive a more precise estimation of the association between p53 codon 72 polymorphism (Arg72Pro, rs1042522 G>C) and cervical cancer risk among Asians...
  29. Yeo M, Lee S, Lee S, Jeon Y, Park S, Cho H, et al. Familial Creutzfeldt-Jakob disease with a mutation at codon 180 presenting with an atypical phenotype. J Clin Neurosci. 2013;20:180-2 pubmed publisher
    The clinical features of familial Creutzfeldt-Jakob disease (fCJD) with a mutation at codon 180 (V180I) are less typical than those of patients with sporadic CJD...
  30. Frenkel Morgenstern M, Danon T, Christian T, Igarashi T, Cohen L, Hou Y, et al. Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels. Mol Syst Biol. 2012;8:572 pubmed publisher
    The cell cycle is a temporal program that regulates DNA synthesis and cell division. When we compared the codon usage of cell cycle-regulated genes with that of other genes, we discovered that there is a significant preference for non-..
  31. Das G, Lyngdoh R. Role of wobble base pair geometry for codon degeneracy: purine-type bases at the anticodon wobble position. J Mol Model. 2012;18:3805-20 pubmed publisher
    b>Codon degeneracy is a key feature of the genetic code, explained by Crick (J Mol Biol 19:548-555, 1966) in terms of imprecision of base pairing at the codon third position (the wobble position) of the codon-anticodon duplex...
  32. Hilterbrand A, Saelens J, Putonti C. CBDB: the codon bias database. BMC Bioinformatics. 2012;13:62 pubmed publisher
    In many genomes, a clear preference in the usage of particular codons exists. The mechanisms that induce codon biases remain an open question; studies have attributed codon usage to translational selection, mutational bias and drift...
  33. Nie X, Lv S, Zhang Y, Du X, Wang L, Biradar S, et al. Complete chloroplast genome sequence of a major invasive species, crofton weed (Ageratina adenophora). PLoS ONE. 2012;7:e36869 pubmed publisher
    ..Repeat structure, codon usage and contraction of the IR were also investigated to reveal the pattern of evolution...
  34. Hart M, Popovic I, Emlet R. Low rates of bindin codon evolution in lecithotrophic Heliocidaris sea urchins. Evolution. 2012;66:1709-21 pubmed publisher
    ..Such responses include high or low rates of codon evolution at gamete recognition loci that encode sperm- and egg-surface peptides...
  35. Cheng X, Wu X, Wang H, Sun Y, Qian Y, Luo L. High codon adaptation in citrus tristeza virus to its citrus host. Virol J. 2012;9:113 pubmed publisher
    ..However, the CTV codon usage was not studied and thus its role in CTV evolution remains unknown...
  36. Williford A, Demuth J. Gene expression levels are correlated with synonymous codon usage, amino acid composition, and gene architecture in the red flour beetle, Tribolium castaneum. Mol Biol Evol. 2012;29:3755-66 pubmed publisher
    ..Here we present results of a genome-wide study of the influence of gene expression on synonymous codon usage, amino acid composition, and gene structure in the red flour beetle, Tribolium castaneum...
  37. Camiolo S, Farina L, Porceddu A. The relation of codon bias to tissue-specific gene expression in Arabidopsis thaliana. Genetics. 2012;192:641-9 pubmed publisher
    The codon composition of coding sequences plays an important role in the regulation of gene expression...
  38. Nougairede A, De Fabritus L, Aubry F, Gould E, Holmes E, de Lamballerie X. Random codon re-encoding induces stable reduction of replicative fitness of Chikungunya virus in primate and mosquito cells. PLoS Pathog. 2013;9:e1003172 pubmed publisher
    Large-scale codon re-encoding represents a powerful method of attenuating viruses to generate safe and cost-effective vaccines...
  39. Tu Y, Wang Y, Wang G, Wu J, Liu Y, Wang S, et al. High-level expression and immunogenicity of a porcine circovirus type 2 capsid protein through codon optimization in Pichia pastoris. Appl Microbiol Biotechnol. 2013;97:2867-75 pubmed publisher
    ..DNA from lymph nodes of postweaning multisystemic wasting syndrome-suffered pigs and synthesized based on the codon bias of the methylotrophic yeast P. pastoris, respectively...
  40. Campos J, Zeng K, Parker D, Charlesworth B, Haddrill P. Codon usage bias and effective population sizes on the X chromosome versus the autosomes in Drosophila melanogaster. Mol Biol Evol. 2013;30:811-23 pubmed publisher
    b>Codon usage bias (CUB) in Drosophila is higher for X-linked genes than for autosomal genes...
  41. Agashe D, Martinez Gomez N, Drummond D, Marx C. Good codons, bad transcript: large reductions in gene expression and fitness arising from synonymous mutations in a key enzyme. Mol Biol Evol. 2013;30:549-60 pubmed publisher
    Biased codon usage in protein-coding genes is pervasive, whereby amino acids are largely encoded by a specific subset of possible codons...
  42. Tumu S, Patil A, Towns W, Dyavaiah M, Begley T. The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four- and five-codon combinations present in Saccharomyces cerevisiae genes. Database (Oxford). 2012;2012:bas002 pubmed publisher
    A codon consists of three nucleotides and functions during translation to dictate the insertion of a specific amino acid in a growing peptide or, in the case of stop codons, to specify the completion of protein synthesis...
  43. Nabiyouni M, Prakash A, Fedorov A. Vertebrate codon bias indicates a highly GC-rich ancestral genome. Gene. 2013;519:113-9 pubmed publisher
    Two factors are thought to have contributed to the origin of codon usage bias in eukaryotes: 1) genome-wide mutational forces that shape overall GC-content and create context-dependent nucleotide bias, and 2) positive selection for ..
  44. Wei J, Zhang Y, Ivanov I, Sachs M. The stringency of start codon selection in the filamentous fungus Neurospora crassa. J Biol Chem. 2013;288:9549-62 pubmed publisher
    ..The stringency of start codon selection impacts the efficiency of initiation at near-cognate codons and the efficiency of initiation at AUG ..
  45. Zhou X, Ruan Z, Huang Q, Tan M, Wang E. Translational fidelity maintenance preventing Ser mis-incorporation at Thr codon in protein from eukaryote. Nucleic Acids Res. 2013;41:302-14 pubmed publisher
    ..the editing function of aaRSs is an indispensable checkpoint excluding non-cognate amino acids at a given codon and ensuring overall translational fidelity...
  46. Salinas T, Duby F, Larosa V, Coosemans N, Bonnefoy N, Motte P, et al. Co-evolution of mitochondrial tRNA import and codon usage determines translational efficiency in the green alga Chlamydomonas. PLoS Genet. 2012;8:e1002946 pubmed publisher
    ..In the unicellular green alga Chlamydomonas, a precise correlation was found between the mitochondrial codon usage and the nature and amount of imported tRNAs...
  47. Tan B, Blanco A, Houston E, Stewart P, Goldmann W, Gill A, et al. Significant differences in incubation times in sheep infected with bovine spongiform encephalopathy result from variation at codon 141 in the PRNP gene. J Gen Virol. 2012;93:2749-56 pubmed publisher
    ..When we segregated sheep according to the amino acid (L or F) encoded at codon 141 of the PRNP gene, the shortest incubation period was observed in LL(141) sheep, whilst incubation periods in ..
  48. Behura S, Severson D. Comparative analysis of codon usage bias and codon context patterns between dipteran and hymenopteran sequenced genomes. PLoS ONE. 2012;7:e43111 pubmed publisher
    b>Codon bias is a phenomenon of non-uniform usage of codons whereas codon context generally refers to sequential pair of codons in a gene...
  49. Zhou J, Gao Z, Sun D, Ding Y, Zhang J, Stipkovits L, et al. A comparative analysis on the synonymous codon usage pattern in viral functional genes and their translational initiation region of ASFV. Virus Genes. 2013;46:271-9 pubmed publisher
    The synonymous codon usage pattern of African swine fever virus (ASFV), the similarity degree of the synonymous codon usage between this virus and some organisms and the synonymous codon usage bias for the translation initiation region ..
  50. Retchless A, Lawrence J. Ecological adaptation in bacteria: speciation driven by codon selection. Mol Biol Evol. 2012;29:3669-83 pubmed publisher
    ..examined orthologous genes in species of Enterobacteriaceae to identify significant differences in the degree of codon selection...
  51. Neves Filho E, Cordeiro D, Vieira A, Rabenhorst S. TP53 codon 72 and intron 3 polymorphisms and mutational status in gastric cancer: an association with tumor onset and prognosis. Pathobiology. 2012;79:323-8 pubmed publisher
    ..have been studied in human tumors, data considering the role of two common TP53 polymorphisms (Pro72Arg in codon 72 and Ins16bp in intron 3) and their associations with TP53 mutations in gastric cancer are very limited...
  52. Xu Y, Ma P, Shah P, Rokas A, Liu Y, Johnson C. Non-optimal codon usage is a mechanism to achieve circadian clock conditionality. Nature. 2013;495:116-20 pubmed publisher
    ..high expression and functional importance, such as the kai genes, are usually encoded by optimal codons, yet the codon-usage bias of the kaiBC genes is not optimized for translational efficiency...
  53. Gil M, Zanetti M, Zoller S, Anisimova M. CodonPhyML: fast maximum likelihood phylogeny estimation under codon substitution models. Mol Biol Evol. 2013;30:1270-80 pubmed publisher
    Markov models of codon substitution naturally incorporate the structure of the genetic code and the selection intensity at the protein level, providing a more realistic representation of protein-coding sequences compared with nucleotide ..