Literature DB >> 15693616

A new classification scheme of the genetic code.

Thomas Wilhelm1, Svetlana Nikolajewa.   

Abstract

Since the early days of the discovery of the genetic code nonrandom patterns have been searched for in the code in the hope of providing information about its origin and early evolution. Here we present a new classification scheme of the genetic code that is based on a binary representation of the purines and pyrimidines. This scheme reveals known patterns more clearly than the common one, for instance, the classification of strong, mixed, and weak codons as well as the ordering of codon families. Furthermore, new patterns have been found that have not been described before: Nearly all quantitative amino acid properties, such as Woese's polarity and the specific volume, show a perfect correlation to Lagerkvist's codon-anticodon binding strength. Our new scheme leads to new ideas about the evolution of the genetic code. It is hypothesized that it started with a binary doublet code and developed via a quaternary doublet code into the contemporary triplet code. Furthermore, arguments are presented against suggestions that a "simpler" code, where only the midbase was informational, was at the origin of the genetic code.

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Year:  2004        PMID: 15693616     DOI: 10.1007/s00239-004-2650-7

Source DB:  PubMed          Journal:  J Mol Evol        ISSN: 0022-2844            Impact factor:   2.395


  59 in total

1.  Testing a biosynthetic theory of the genetic code: fact or artifact?

Authors:  T A Ronneberg; L F Landweber; S J Freeland
Journal:  Proc Natl Acad Sci U S A       Date:  2000-12-05       Impact factor: 11.205

2.  The origin of the genetic code and protein synthesis.

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Journal:  J Mol Evol       Date:  1997-10       Impact factor: 2.395

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Journal:  J Mol Evol       Date:  1998-07       Impact factor: 2.395

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Journal:  Arch Biochem Biophys       Date:  1974-04-02       Impact factor: 4.013

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7.  Correlation of Tm, sequence, and delta H of complementary RNA helices and comparison with DNA helices.

Authors:  R L Ornstein; J R Fresco
Journal:  Biopolymers       Date:  1983-08       Impact factor: 2.505

Review 8.  Unorthodox codon reading and the evolution of the genetic code.

Authors:  U Lagerkvist
Journal:  Cell       Date:  1981-02       Impact factor: 41.582

9.  The hypercycle. A principle of natural self-organization. Part A: Emergence of the hypercycle.

Authors:  M Eigen; P Schuster
Journal:  Naturwissenschaften       Date:  1977-11

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Authors:  P Dunnill
Journal:  Nature       Date:  1966-06-18       Impact factor: 49.962

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  9 in total

1.  A model-independent approach to infer hierarchical codon substitution dynamics.

Authors:  Olof Görnerup; Martin Nilsson Jacobi
Journal:  BMC Bioinformatics       Date:  2010-04-23       Impact factor: 3.169

2.  Common patterns in type II restriction enzyme binding sites.

Authors:  Svetlana Nikolajewa; Andreas Beyer; Maik Friedel; Jens Hollunder; Thomas Wilhelm
Journal:  Nucleic Acids Res       Date:  2005-05-11       Impact factor: 16.971

3.  Human Retrovirus Codon Usage from tRNA Point of View: Therapeutic Insights.

Authors:  Diego Frias; Joana P Monteiro-Cunha; Aline C Mota-Miranda; Vagner S Fonseca; Tulio de Oliveira; Bernardo Galvao-Castro; Luiz C J Alcantara
Journal:  Bioinform Biol Insights       Date:  2013-10-10

4.  On the organizational dynamics of the genetic code.

Authors:  Zhang Zhang; Jun Yu
Journal:  Genomics Proteomics Bioinformatics       Date:  2011-04       Impact factor: 7.691

5.  Statistical analysis of pentose phosphate pathway genes from eubacteria and eukarya reveals translational selection as a major force in shaping codon usage pattern.

Authors:  Ayon Pal; Subhasis Mukhopadhyay; Asim Kumar Bothra
Journal:  Bioinformation       Date:  2013-04-13

6.  Codon size reduction as the origin of the triplet genetic code.

Authors:  Pavel V Baranov; Maxime Venin; Gregory Provan
Journal:  PLoS One       Date:  2009-05-27       Impact factor: 3.240

Review 7.  An integrated, structure- and energy-based view of the genetic code.

Authors:  Henri Grosjean; Eric Westhof
Journal:  Nucleic Acids Res       Date:  2016-07-22       Impact factor: 16.971

8.  A content-centric organization of the genetic code.

Authors:  Jun Yu
Journal:  Genomics Proteomics Bioinformatics       Date:  2007-02       Impact factor: 7.691

9.  Circular Tessera Codes in the Evolution of the Genetic Code.

Authors:  Elena Fimmel; Martin Starman; Lutz Strüngmann
Journal:  Bull Math Biol       Date:  2020-04-04       Impact factor: 1.758

  9 in total

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