Literature DB >> 28090420

The "periodic table" of the genetic code: A new way to look at the code and the decoding process.

Anton A Komar1.   

Abstract

Henri Grosjean and Eric Westhof recently presented an information-rich, alternative view of the genetic code, which takes into account current knowledge of the decoding process, including the complex nature of interactions between mRNA, tRNA and rRNA that take place during protein synthesis on the ribosome, and it also better reflects the evolution of the code. The new asymmetrical circular genetic code has a number of advantages over the traditional codon table and the previous circular diagrams (with a symmetrical/clockwise arrangement of the U, C, A, G bases). Most importantly, all sequence co-variances can be visualized and explained based on the internal logic of the thermodynamics of codon-anticodon interactions.

Keywords:  aminoacyl-tRNAs; circular genetic code diagram; decoding; energetics of codon-anticodon interactions; genetic code; genetic code evolution

Year:  2016        PMID: 28090420      PMCID: PMC5173307          DOI: 10.1080/21690731.2016.1234431

Source DB:  PubMed          Journal:  Translation (Austin)        ISSN: 2169-0731


  14 in total

Review 1.  One core, two shells: bacterial and eukaryotic ribosomes.

Authors:  Sergey Melnikov; Adam Ben-Shem; Nicolas Garreau de Loubresse; Lasse Jenner; Gulnara Yusupova; Marat Yusupov
Journal:  Nat Struct Mol Biol       Date:  2012-06-05       Impact factor: 15.369

Review 2.  What recent ribosome structures have revealed about the mechanism of translation.

Authors:  T Martin Schmeing; V Ramakrishnan
Journal:  Nature       Date:  2009-10-18       Impact factor: 49.962

3.  A Tetrahedral Representation of the Genetic Code Emphasizing Aspects of Symmetry.

Authors:  Fernando Castro-Chavez
Journal:  BIOcomplexity       Date:  2012-06-29

Review 4.  Dual functions of codons in the genetic code.

Authors:  Alexey V Lobanov; Anton A Turanov; Dolph L Hatfield; Vadim N Gladyshev
Journal:  Crit Rev Biochem Mol Biol       Date:  2010-08       Impact factor: 8.250

Review 5.  The use of unnatural amino acids to study and engineer protein function.

Authors:  Petra Neumann-Staubitz; Heinz Neumann
Journal:  Curr Opin Struct Biol       Date:  2016-06-17       Impact factor: 6.809

6.  RNA codewords and protein synthesis, VII. On the general nature of the RNA code.

Authors:  M Nirenberg; P Leder; M Bernfield; R Brimacombe; J Trupin; F Rottman; C O'Neal
Journal:  Proc Natl Acad Sci U S A       Date:  1965-05       Impact factor: 11.205

7.  The molecular basis for the genetic code.

Authors:  C R Woese; D H Dugre; W C Saxinger; S A Dugre
Journal:  Proc Natl Acad Sci U S A       Date:  1966-04       Impact factor: 11.205

Review 8.  Genetic code flexibility in microorganisms: novel mechanisms and impact on physiology.

Authors:  Jiqiang Ling; Patrick O'Donoghue; Dieter Söll
Journal:  Nat Rev Microbiol       Date:  2015-09-22       Impact factor: 60.633

Review 9.  Structural basis of the translational elongation cycle.

Authors:  Rebecca M Voorhees; V Ramakrishnan
Journal:  Annu Rev Biochem       Date:  2013       Impact factor: 23.643

Review 10.  Non-Standard Genetic Codes Define New Concepts for Protein Engineering.

Authors:  Ana R Bezerra; Ana R Guimarães; Manuel A S Santos
Journal:  Life (Basel)       Date:  2015-11-12
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  2 in total

1.  Queuosine-modified tRNAs confer nutritional control of protein translation.

Authors:  Francesca Tuorto; Carine Legrand; Cansu Cirzi; Giuseppina Federico; Reinhard Liebers; Martin Müller; Ann E Ehrenhofer-Murray; Gunnar Dittmar; Hermann-Josef Gröne; Frank Lyko
Journal:  EMBO J       Date:  2018-08-09       Impact factor: 11.598

2.  Effects of codon optimization on coagulation factor IX translation and structure: Implications for protein and gene therapies.

Authors:  Aikaterini Alexaki; Gaya K Hettiarachchi; John C Athey; Upendra K Katneni; Vijaya Simhadri; Nobuko Hamasaki-Katagiri; Puja Nanavaty; Brian Lin; Kazuyo Takeda; Darón Freedberg; Dougald Monroe; Joseph R McGill; Robert Peters; Jacob M Kames; David D Holcomb; Ryan C Hunt; Zuben E Sauna; Amy Gelinas; Nebojsa Janjic; Michael DiCuccio; Haim Bar; Anton A Komar; Chava Kimchi-Sarfaty
Journal:  Sci Rep       Date:  2019-10-29       Impact factor: 4.379

  2 in total

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