On the coevolution of genes and genetic code.

The canonical genetic code acts efficiently in minimizing the effects of mistranslations and point mutations. In the work presented we have also considered the effects of single nucleotide insertions and deletions on the optimality of the genetic code. Our results suggest that the canonical genetic code compensates for the ins/del mutations as well as mistranslations and point mutations. On the other hand, we highlighted the point that ins/del mutations have a lesser impact on the selected genes of Saccharomyces cerevisiae compared to randomly generated ones. We hypothesized that the codon usage preferences in S. cerevisiae genes are responsible for the higher efficiency of translation machinery in this organism. Our results support the conjecture that codon usage preferences render the genetic code more effective in minimizing the effects of ins/del mutations.

[1]  Serge Massar,et al.  Optimality of the genetic code with respect to protein stability and amino-acid frequencies , 2001, Genome Biology.

[2]  D. Söll,et al.  Protein biosynthesis in organelles requires misaminoacylation of tRNA , 1988, Nature.

[3]  Massimo Di Giulio,et al.  The Coevolution Theory of the Origin of the Genetic Code , 1999 .

[4]  H. Najafabadi,et al.  Optimality of codon usage in Escherichia coli due to load minimization. , 2005, Journal of theoretical biology.

[5]  L. Hurst,et al.  The Genetic Code Is One in a Million , 1998, Journal of Molecular Evolution.

[6]  R S Root-Bernstein.  On the origin of the genetic code. , 1982, Journal of theoretical biology.

[7]  M. Shimizu.  Molecular basis for the genetic code , 2005, Journal of Molecular Evolution.

[8]  H. Goodarzi,et al.  On the optimality of the genetic code, with the consideration of termination codons. , 2004, Bio Systems.

[9]  Stephen J. Freeland,et al.  The Darwinian Genetic Code: An Adaptation for Adapting? , 2002, Genetic Programming and Evolvable Machines.

[10]  W. Fitch,et al.  The phylogeny of tRNA sequences provides evidence for ambiguity reduction in the origin of the genetic code. , 1987, Cold Spring Harbor symposia on quantitative biology.

[11]  V. Bryson,et al.  Evolving Genes and Proteins. , 1965, Science.

[12]  F. Taylor,et al.  The code within the codons. , 1989, Bio Systems.

[13]  J. Wong.  A co-evolution theory of the genetic code. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[14]  L F Landweber,et al.  Measuring adaptation within the genetic code. , 2000, Trends in biochemical sciences.

[15]  Massimo Di Giulio,et al.  The origin of the genetic code cannot be studied using measurements based on the PAM matrix because this matrix reflects the code itself, making any such analyses tautologous. , 2001 .

[16]  R. Curnow,et al.  The evolution of the genetic code. , 1976, Biochimie.

[17]  S. Osawa,et al.  Recent evidence for evolution of the genetic code , 1992, Microbiological reviews.

[18]  M. Archetti.  Selection on Codon Usage for Error Minimization at the Protein Level , 2004, Journal of Molecular Evolution.

[19]  A. Goldberg,et al.  Genetic Code: Aspects of Organization , 1966, Science.

[20]  C. Woese.  The genetic code : the molecular basis for genetic expression , 1967 .

[21]  C. Woese,et al.  Evolution of the genetic code , 2004, The Science of Nature.

[22]  S A Benner,et al.  Amino acid substitution during functionally constrained divergent evolution of protein sequences. , 1994, Protein engineering.

[23]  Chen-Tseh Zhu,et al.  Codon Usage Decreases the Error Minimization Within the Genetic Code , 2003, Journal of Molecular Evolution.

[24]  M. Di Giulio,et al.  The Robust Statistical Bases of the Coevolution Theory of Genetic Code Origin , 2000, Journal of Molecular Evolution.

[25]  W. Fitch.  Evidence suggesting a partial, internal duplication in the ancestral gene for heme-containing globins. , 1966, Journal of molecular biology.

[26]  J. L. King,et al.  Non-Darwinian evolution. , 1969, Science.

[27]  C. Epstein,et al.  Role of the Amino-Acid ‘Code’ and of Selection for Conformation in the Evolution of Proteins , 1966, Nature.

[28]  V. Chechetkin,et al.  Block structure and stability of the genetic code. , 2003, Journal of theoretical biology.

[29]  J. Parker,et al.  Errors and alternatives in reading the universal genetic code. , 1989, Microbiological reviews.

[30]  L F Landweber,et al.  Rhyme or reason: RNA-arginine interactions and the genetic code. , 1998, Chemistry & biology.

[31]  M. Kimura.  A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences , 1980, Journal of Molecular Evolution.

[32]  H. Najafabadi,et al.  The impact of including tRNA content on the optimality of the genetic code , 2005, Bulletin of mathematical biology.

[33]  S. Pestka,et al.  On the Coding of Genetic Information , 1963 .

[34]  Laurence D. Hurst,et al.  A quantitative measure of error minimization in the genetic code , 1991, Journal of Molecular Evolution.

[35]  W. Gilbert,et al.  STREPTOMYCIN, SUPPRESSION, AND THE CODE. , 1964, Proceedings of the National Academy of Sciences of the United States of America.

[36]  S. R. Pelc,et al.  Stereochemical Relationship Between Coding Triplets and Amino-Acids , 1966, Nature.

[37]  Massimo Di Giulio,et al.  The origin of the genetic code: theories and their relationships, a review. , 2005 .

[38]  C. Woese,et al.  On the fundamental nature and evolution of the genetic code. , 1966, Cold Spring Harbor symposia on quantitative biology.

[39]  J. Hopfield.  Origin of the genetic code: a testable hypothesis based on tRNA structure, sequence, and kinetic proofreading. , 1978, Proceedings of the National Academy of Sciences of the United States of America.

[40]  L. Pauling,et al.  Evolutionary Divergence and Convergence in Proteins , 1965 .

[41]  C. Alff-Steinberger,et al.  The genetic code and error transmission. , 1969, Proceedings of the National Academy of Sciences of the United States of America.

[42]  T. Steitz,et al.  Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. , 1986, Annual review of biophysics and biophysical chemistry.

[43]  C. Tanford,et al.  The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale. , 1971, The Journal of biological chemistry.

[44]  David H. Ardell,et al.  On Error Minimization in a Sequential Origin of the Standard Genetic Code , 1998, Journal of Molecular Evolution.

[45]  H. Khorana,et al.  A further study of misreading of codons induced by streptomycin and neomycin using ribopolynucleotides containing two nucleotides in alternating sequence as templates. , 1966, Journal of molecular biology.

[46]  Massimo Di Giulio,et al.  Genetic code origin and the strength of natural selection. , 2000 .

[47]  F. Crick.  Origin of the Genetic Code , 1967, Nature.

[48]  R. Doolittle,et al.  A simple method for displaying the hydropathic character of a protein. , 1982, Journal of molecular biology.

[49]  Nick Goldman,et al.  Further results on error minimization in the genetic code , 1993, Journal of Molecular Evolution.

[50]  L F Landweber,et al.  Selection, history and chemistry: the three faces of the genetic code. , 1999, Trends in biochemical sciences.

[51]  C R Woese,et al.  Evolution of the genetic code , 1973, The Science of Nature.

[52]  R. Swanson.  A unifying concept for the amino acid code. , 1984, Bulletin of mathematical biology.

[53]  E. Szathmáry,et al.  Coding coenzyme handles: a hypothesis for the origin of the genetic code. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[54]  T. M. Sonneborn.  Degeneracy of the Genetic Code: Extent, Nature, and Genetic Implications , 1965 .

[55]  H. Echols,et al.  Fidelity mechanisms in DNA replication. , 1991, Annual review of biochemistry.