genetic code

Summary

Summary: The meaning ascribed to the BASE SEQUENCE with respect to how it is translated into AMINO ACID SEQUENCE. The start, stop, and order of amino acids of a protein is specified by consecutive triplets of nucleotides called codons (CODON).

Top Publications

  1. Zhou X, Fang Z, Ruan Z, Wang M, Liu R, Tan M, et al. Aminoacylation and translational quality control strategy employed by leucyl-tRNA synthetase from a human pathogen with genetic code ambiguity. Nucleic Acids Res. 2013;41:9825-38 pubmed publisher
  2. Chen P, Groff D, Guo J, Ou W, Cellitti S, Geierstanger B, et al. A facile system for encoding unnatural amino acids in mammalian cells. Angew Chem Int Ed Engl. 2009;48:4052-5 pubmed publisher
    ..Transfer of this orthogonal tRNA-aaRS pair into mammalian cells made possible the selective incorporation of this unnatural amino acid into proteins. ..
  3. Schimmel P. Mistranslation and its control by tRNA synthetases. Philos Trans R Soc Lond B Biol Sci. 2011;366:2965-71 pubmed publisher
    ..During translation, they establish the rules of the genetic code, whereby each amino acid is attached to a tRNA that is cognate to the amino acid...
  4. Rodin A, Szathmary E, Rodin S. On origin of genetic code and tRNA before translation. Biol Direct. 2011;6:14 pubmed publisher
    Synthesis of proteins is based on the genetic code - a nearly universal assignment of codons to amino acids (aas). A major challenge to the understanding of the origins of this assignment is the archetypal "key-lock vs...
  5. Yarus M, Widmann J, Knight R. RNA-amino acid binding: a stereochemical era for the genetic code. J Mol Evol. 2009;69:406-29 pubmed publisher
    ..Such amino acid sites can be queried for parallels to the genetic code. Using recent sequences for 337 independent binding sites directed to 8 amino acids and containing 18,551 ..
  6. Carter C. Whence the genetic code? Thawing the 'frozen accident'. Heredity (Edinb). 2008;100:339-40 pubmed publisher
  7. Bezerra A, Simões J, Lee W, Rung J, Weil T, Gut I, et al. Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification. Proc Natl Acad Sci U S A. 2013;110:11079-84 pubmed publisher
    ..How these fungi survived this potentially lethal genetic code alteration and its relevance for their biology are not understood...
  8. Hlevnjak M, Polyansky A, Zagrovic B. Sequence signatures of direct complementarity between mRNAs and cognate proteins on multiple levels. Nucleic Acids Res. 2012;40:8874-82 pubmed publisher
    ..physico-chemical properties of mRNAs and cognate proteins, with implications concerning both the origin of the genetic code and mRNA-protein interactions, is unexplored...
  9. Pereira P, Magnol L, Sahún I, Brault V, Duchon A, Prandini P, et al. A new mouse model for the trisomy of the Abcg1-U2af1 region reveals the complexity of the combinatorial genetic code of down syndrome. Hum Mol Genet. 2009;18:4756-69 pubmed publisher
    ..Our work unravels the complexity of combinatorial genetic code modulating different aspect of mental retardation in DS patients...

More Information

Publications62

  1. Drummond D, Wilke C. The evolutionary consequences of erroneous protein synthesis. Nat Rev Genet. 2009;10:715-24 pubmed publisher
    ..Evolutionary responses to errors fall into two broad categories: adaptations that minimize errors and their attendant costs and adaptations that exploit errors for the organism's benefit. ..
  2. Davis L, Chin J. Designer proteins: applications of genetic code expansion in cell biology. Nat Rev Mol Cell Biol. 2012;13:168-82 pubmed publisher
    ..This has allowed new biological insights into protein conformational changes, protein interactions, elementary processes in signal transduction and the role of post-translational modifications. ..
  3. Johnson D, Wang L. Imprints of the genetic code in the ribosome. Proc Natl Acad Sci U S A. 2010;107:8298-303 pubmed publisher
    The establishment of the genetic code remains elusive nearly five decades after the code was elucidated...
  4. Bender A, Hajieva P, Moosmann B. Adaptive antioxidant methionine accumulation in respiratory chain complexes explains the use of a deviant genetic code in mitochondria. Proc Natl Acad Sci U S A. 2008;105:16496-501 pubmed publisher
    ..Despite the pivotal role of the genetic code for cell biology, the functional significance of the deviant mitochondrial code has remained enigmatic since ..
  5. Turanov A, Xu X, Carlson B, Yoo M, Gladyshev V, Hatfield D. Biosynthesis of selenocysteine, the 21st amino acid in the genetic code, and a novel pathway for cysteine biosynthesis. Adv Nutr. 2011;2:122-8 pubmed publisher
    The biosynthetic pathway for selenocysteine (Sec), the 21st amino acid in the genetic code whose codeword is UGA, was recently determined in eukaryotes and archaea...
  6. Caetano Anolles G, Seufferheld M. The coevolutionary roots of biochemistry and cellular organization challenge the RNA world paradigm. J Mol Microbiol Biotechnol. 2013;23:152-77 pubmed publisher
    ..This changes the perception we have of the rise of modern biochemistry and prompts further analysis of the emergence of biological complexity in an ever-expanding coevolving world of macromolecules. ..
  7. Higgs P, Pudritz R. A thermodynamic basis for prebiotic amino acid synthesis and the nature of the first genetic code. Astrobiology. 2009;9:483-90 pubmed publisher
    ..of the early amino acids were most likely reflected in the composition of the first proteins at the time the genetic code originated...
  8. Wang Q, Parrish A, Wang L. Expanding the genetic code for biological studies. Chem Biol. 2009;16:323-36 pubmed publisher
    ..Genetic incorporation of unnatural amino acids provides a powerful method for investigating a wide variety of biological processes both in vitro and in vivo. ..
  9. Jestin J, Kempf A. Optimization models and the structure of the genetic code. J Mol Evol. 2009;69:452-7 pubmed publisher
    The codon assignment of the quasi-universal genetic code can be assumed to have resulted from the evolutionary pressures that prevailed when the code was still evolving...
  10. Moura G, Carreto L, Santos M. Genetic code ambiguity: an unexpected source of proteome innovation and phenotypic diversity. Curr Opin Microbiol. 2009;12:631-7 pubmed publisher
    ..A brief introduction to the molecular nature of translational error is provided; however, detailed information on the mechanistic aspects of mistranslation or comprehensive literature reviews of this topic should be obtained elsewhere. ..
  11. Grosjean H, De Crecy Lagard V, Marck C. Deciphering synonymous codons in the three domains of life: co-evolution with specific tRNA modification enzymes. FEBS Lett. 2010;584:252-64 pubmed publisher
    ..an essential role in the progressive introduction of new amino acids, and in the refinement and standardization of the canonical nuclear genetic code observed in all extant organisms (functional convergent evolutionary hypothesis).
  12. Santos M, Gomes A, Santos M, Carreto L, Moura G. The genetic code of the fungal CTG clade. C R Biol. 2011;334:607-11 pubmed publisher
    b>Genetic code alterations discovered over the last 40 years in bacteria and eukaryotes invalidate the hypothesis that the code is universal and frozen...
  13. Ling J, So B, Yadavalli S, Roy H, Shoji S, Fredrick K, et al. Resampling and editing of mischarged tRNA prior to translation elongation. Mol Cell. 2009;33:654-60 pubmed publisher
    Faithful translation of the genetic code depends on the GTPase EF-Tu delivering correctly charged aminoacyl-tRNAs to the ribosome for pairing with cognate codons...
  14. Wang K, Schmied W, Chin J. Reprogramming the genetic code: from triplet to quadruplet codes. Angew Chem Int Ed Engl. 2012;51:2288-97 pubmed publisher
    The genetic code of cells is near-universally triplet, and since many ribosomal mutations are lethal, changing the cellular ribosome to read nontriplet codes is challenging...
  15. Ohama T, Inagaki Y, Bessho Y, Osawa S. Evolving genetic code. Proc Jpn Acad Ser B Phys Biol Sci. 2008;84:58-74 pubmed
    In 1985, we reported that a bacterium, Mycoplasma capricolum, used a deviant genetic code, namely UGA, a "universal" stop codon, was read as tryptophan...
  16. Parrish A, She X, Xiang Z, Coin I, Shen Z, Briggs S, et al. Expanding the genetic code of Caenorhabditis elegans using bacterial aminoacyl-tRNA synthetase/tRNA pairs. ACS Chem Biol. 2012;7:1292-302 pubmed publisher
    The genetic code specifies 20 common amino acids and is largely preserved in both single and multicellular organisms...
  17. Agris P. Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications. EMBO Rep. 2008;9:629-35 pubmed publisher
    ..This concept reduces an entropic penalty for translation and provides a physicochemical basis for the conservation of RNA modifications in general. ..
  18. Mathew D, Luthey Schulten Z. On the physical basis of the amino acid polar requirement. J Mol Evol. 2008;66:519-28 pubmed publisher
    ..became associated with their specific amino acids is fundamental to deriving a theory for the origin of the genetic code. Carl Woese and coworkers designed a series of experiments to test associations between amino acids and ..
  19. Zhang Z, Yu J. On the organizational dynamics of the genetic code. Genomics Proteomics Bioinformatics. 2011;9:21-9 pubmed publisher
    The organization of the canonical genetic code needs to be thoroughly illuminated...
  20. Kawahara Kobayashi A, Masuda A, Araiso Y, Sakai Y, Kohda A, Uchiyama M, et al. Simplification of the genetic code: restricted diversity of genetically encoded amino acids. Nucleic Acids Res. 2012;40:10576-84 pubmed publisher
    At earlier stages in the evolution of the universal genetic code, fewer than 20 amino acids were considered to be used...
  21. Alkatib S, Scharff L, Rogalski M, Fleischmann T, Matthes A, Seeger S, et al. The contributions of wobbling and superwobbling to the reading of the genetic code. PLoS Genet. 2012;8:e1003076 pubmed publisher
    ..and mitochondria) do not encode the full set of 32 tRNA species required to read all triplets of the genetic code according to the conventional wobble rules...
  22. Yu J. A content-centric organization of the genetic code. Genomics Proteomics Bioinformatics. 2007;5:1-6 pubmed
    The codon table for the canonical genetic code can be rearranged in such a way that the code is divided into four quarters and two halves according to the variability of their GC and purine contents, respectively...
  23. Abascal F, Zardoya R, Posada D. Genetic code prediction for metazoan mitochondria with GenDecoder. Methods Mol Biol. 2009;537:233-42 pubmed publisher
    There is a standard genetic code that is used by most organisms, but exceptions exist in which particular codons are translated with a different meaning, i.e., as a different amino acid...
  24. Di Giulio M. An extension of the coevolution theory of the origin of the genetic code. Biol Direct. 2008;3:37 pubmed publisher
    The coevolution theory of the origin of the genetic code suggests that the genetic code is an imprint of the biosynthetic relationships between amino acids...
  25. Whelan S. The genetic code can cause systematic bias in simple phylogenetic models. Philos Trans R Soc Lond B Biol Sci. 2008;363:4003-11 pubmed publisher
    ..describe their evolution do not explicitly account for the dependencies between sites in a codon induced by the genetic code. This study evaluates the performance of several standard methods on datasets simulated under a simple ..
  26. Turanov A, Lobanov A, Fomenko D, Morrison H, Sogin M, Klobutcher L, et al. Genetic code supports targeted insertion of two amino acids by one codon. Science. 2009;323:259-61 pubmed publisher
    Strict one-to-one correspondence between codons and amino acids is thought to be an essential feature of the genetic code. However, we report that one codon can code for two different amino acids with the choice of the inserted amino acid ..
  27. Fournier G, Neumann J, Gogarten J. Inferring the ancient history of the translation machinery and genetic code via recapitulation of ribosomal subunit assembly orders. PLoS ONE. 2010;5:e9437 pubmed publisher
    ..in ribosomal proteins have significant biases in amino acid usage, likely indicating the expansion of the genetic code at the time leading up to the most recent common ancestor(s) (MRCA)...
  28. Miranda I, Rocha R, Santos M, Mateus D, Moura G, Carreto L, et al. A genetic code alteration is a phenotype diversity generator in the human pathogen Candida albicans. PLoS ONE. 2007;2:e996 pubmed
    The discovery of genetic code alterations and expansions in both prokaryotes and eukaryotes abolished the hypothesis of a frozen and universal genetic code and exposed unanticipated flexibility in codon and amino acid assignments...
  29. Ohta A, Murakami H, Higashimura E, Suga H. Synthesis of polyester by means of genetic code reprogramming. Chem Biol. 2007;14:1315-22 pubmed
    Here we report the ribosomal polymerization of alpha-hydroxy acids by means of genetic code reprogramming...
  30. Goto Y, Katoh T, Suga H. Flexizymes for genetic code reprogramming. Nat Protoc. 2011;6:779-90 pubmed publisher
    b>Genetic code reprogramming is a method for the reassignment of arbitrary codons from proteinogenic amino acids to nonproteinogenic ones; thus, specific sequences of nonstandard peptides can be ribosomally expressed according to their mRNA ..
  31. Ikehara K, Niihara Y. Origin and evolutionary process of the genetic code. Curr Med Chem. 2007;14:3221-31 pubmed
    The genetic code plots the relationship between a triplet base sequence on RNA and an amino acid that corresponds to a protein associated with a required function in organisms...
  32. Bianco A, Townsley F, Greiss S, Lang K, Chin J. Expanding the genetic code of Drosophila melanogaster. Nat Chem Biol. 2012;8:748-50 pubmed publisher
    b>Genetic code expansion for unnatural amino acid mutagenesis has, until recently, been limited to cell culture...
  33. Fournier G, Andam C, Alm E, Gogarten J. Molecular evolution of aminoacyl tRNA synthetase proteins in the early history of life. Orig Life Evol Biosph. 2011;41:621-32 pubmed publisher
    ..reconstruction of their pre-LUCA ancestors can reveal the evolutionary processes at work in the origin of the genetic code. In particular, sequence reconstructions of the paralog ancestors of isoleucyl- and valyl- RS provide strong ..
  34. Russell R, Beckenbach A. Recoding of translation in turtle mitochondrial genomes: programmed frameshift mutations and evidence of a modified genetic code. J Mol Evol. 2008;67:682-95 pubmed publisher
  35. Firnberg E, Ostermeier M. The genetic code constrains yet facilitates Darwinian evolution. Nucleic Acids Res. 2013;41:7420-8 pubmed publisher
    ..Here, we address the extent to which the structure of the standard genetic code constrains evolution by analyzing adaptive mutations of the antibiotic resistance gene TEM-1 ?-lactamase and ..
  36. Subramaniam A, Pan T, Cluzel P. Environmental perturbations lift the degeneracy of the genetic code to regulate protein levels in bacteria. Proc Natl Acad Sci U S A. 2013;110:2419-24 pubmed publisher
    The genetic code underlying protein synthesis is a canonical example of a degenerate biological system...
  37. Xiao J, Yu J. A scenario on the stepwise evolution of the genetic code. Genomics Proteomics Bioinformatics. 2007;5:143-51 pubmed publisher
    ..adenosine, uridine, and guanosine) and two (adenosine and uridine) nucleosides, respectively, so that the genetic code started uncomplicated...
  38. Hoesl M, Budisa N. Recent advances in genetic code engineering in Escherichia coli. Curr Opin Biotechnol. 2012;23:751-7 pubmed publisher
    The expansion of the genetic code is gradually becoming a core discipline in Synthetic Biology...
  39. Higgs P. A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code. Biol Direct. 2009;4:16 pubmed publisher
    The arrangement of the amino acids in the genetic code is such that neighbouring codons are assigned to amino acids with similar physical properties...
  40. Butler T, Goldenfeld N, Mathew D, Luthey Schulten Z. Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement. Phys Rev E Stat Nonlin Soft Matter Phys. 2009;79:060901 pubmed
    A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an ..
  41. Hamashima K, Fujishima K, Masuda T, Sugahara J, Tomita M, Kanai A. Nematode-specific tRNAs that decode an alternative genetic code for leucine. Nucleic Acids Res. 2012;40:3653-62 pubmed publisher
    ..Our findings provide the first example of unexpected tRNAs that do not consistently obey the general translation rules for higher eukaryotes. ..
  42. Shah P, Gilchrist M. Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift. Proc Natl Acad Sci U S A. 2011;108:10231-6 pubmed publisher
    The genetic code is redundant with most amino acids using multiple codons. In many organisms, codon usage is biased toward particular codons...
  43. Matsumoto T, Ishikawa S, Hashimoto T, Inagaki Y. A deviant genetic code in the green alga-derived plastid in the dinoflagellate Lepidodinium chlorophorum. Mol Phylogenet Evol. 2011;60:68-72 pubmed publisher
    We here report a deviant genetic code, in which AUA is read as methionine (Met) instead of isoleucine (Ile), in the green alga-derived plastid in the dinoflagellate Lepidodinium chlorophorum. Although L...
  44. Sanchez R, Grau R. An algebraic hypothesis about the primeval genetic code architecture. Math Biosci. 2009;221:60-76 pubmed publisher
    A plausible architecture of an ancient genetic code is derived from an extended base triplet vector space over the Galois field of the extended base alphabet {D,A,C,G,U}, where symbol D represents one or more hypothetical bases with ..
  45. Tlusty T. A colorful origin for the genetic code: information theory, statistical mechanics and the emergence of molecular codes. Phys Life Rev. 2010;7:362-76 pubmed publisher
    The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. While the biochemical details of this code were unraveled long ago, its origin is still obscure...
  46. Kille S, Acevedo Rocha C, Parra L, Zhang Z, Opperman D, Reetz M, et al. Reducing codon redundancy and screening effort of combinatorial protein libraries created by saturation mutagenesis. ACS Synth Biol. 2013;2:83-92 pubmed publisher
    ..We show that this strategy is suitable for any saturation mutagenesis methodology to generate less-redundant libraries. ..
  47. Di Giulio M. The origin of the genetic code in the ocean abysses: new comparisons confirm old observations. J Theor Biol. 2013;333:109-16 pubmed publisher
    ..Indeed, the pattern deriving from a different pair of such organisms led to establish that the origin of the genetic code might have occurred in the ocean abysses...
  48. Jestin J, Soulé C. Symmetries by base substitutions in the genetic code predict 2(') or 3(') aminoacylation of tRNAs. J Theor Biol. 2007;247:391-4 pubmed
  49. Moura G, Paredes J, Santos M. Development of the genetic code: insights from a fungal codon reassignment. FEBS Lett. 2010;584:334-41 pubmed publisher
    The high conservation of the genetic code and its fundamental role in genome decoding suggest that its evolution is highly restricted or even frozen...
  50. Church G, Gao Y, Kosuri S. Next-generation digital information storage in DNA. Science. 2012;337:1628 pubmed
    ..We developed a strategy to encode arbitrary digital information in DNA, wrote a 5.27-megabit book using DNA microchips, and read the book by using next-generation DNA sequencing. ..
  51. Gile G, Novis P, Cragg D, Zuccarello G, Keeling P. The distribution of Elongation Factor-1 Alpha (EF-1alpha), Elongation Factor-Like (EFL), and a non-canonical genetic code in the ulvophyceae: discrete genetic characters support a consistent phylogenetic framework. J Eukaryot Microbiol. 2009;56:367-72 pubmed publisher
    ..Second, the nuclear genomes of dasycladaleans A. acetabulum and Batophora oerstedii use a rare non-canonical genetic code in which the canonical termination codons TAA and TAG instead encode glutamine...
  52. Ye S, Riou M, Carvalho S, Paoletti P. Expanding the genetic code in Xenopus laevis oocytes. Chembiochem. 2013;14:230-5 pubmed publisher
    ..Our method should be generally applicable to studies of other LGICs in Xenopus oocytes...
  53. Bacher J, Waas W, Metzgar D, De Crecy Lagard V, Schimmel P. Genetic code ambiguity confers a selective advantage on Acinetobacter baylyi. J Bacteriol. 2007;189:6494-6 pubmed
    A primitive genetic code, composed of a smaller set of amino acids, may have expanded via recursive periods of genetic code ambiguity that were followed by specificity...