On the evolution of the standard amino-acid alphabet

Although one standard amino-acid 'alphabet' is used by most organisms on Earth, the evolutionary cause(s) and significance of this alphabet remain elusive. Fresh insights into the origin of the alphabet are now emerging from disciplines as diverse as astrobiology, biochemical engineering and bioinformatics.

[1]  M. Baumann,et al.  Techniques for studying protein heterogeneity and post-translational modifications , 2004, Expert review of proteomics.

[2]  M. Lynch.  Simple evolutionary pathways to complex proteins , 2005, Protein science : a publication of the Protein Society.

[3]  M. Legge,et al.  The protein folds as platonic forms: new support for the pre-Darwinian conception of evolution by natural law. , 2002, Journal of theoretical biology.

[4]  M J Dufton,et al.  Genetic code synonym quotas and amino acid complexity: cutting the cost of proteins? , 1997, Journal of theoretical biology.

[5]  Michele Vendruscolo,et al.  Neutral evolution of model proteins: diffusion in sequence space and overdispersion. , 1998, Journal of theoretical biology.

[6]  E. Szathmáry,et al.  The origin of the genetic code: amino acids as cofactors in an RNA world. , 1999, Trends in genetics : TIG.

[7]  J. Wong,et al.  Coevolution theory of the genetic code at age thirty. , 2005, BioEssays : news and reviews in molecular, cellular and developmental biology.

[8]  Michael E. Hahn,et al.  Manipulating proteins with chemistry: a cross-section of chemical biology. , 2005, Trends in biochemical sciences.

[9]  Takashi Gojobori,et al.  Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[10]  R. B. Vilim,et al.  Fold-specific substitution matrices for protein classification , 2004, Bioinform..

[11]  S. Benner,et al.  Is there a common chemical model for life in the universe? , 2004, Current opinion in chemical biology.

[12]  Ke Fan,et al.  What is the minimum number of letters required to fold a protein? , 2003, Journal of molecular biology.

[13]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[14]  E N Trifonov,et al.  Consensus temporal order of amino acids and evolution of the triplet code. , 2000, Gene.

[15]  Marek Kimmel,et al.  Analysis of differences in amino acid substitution patterns, using multilevel G-tests. , 2005, Comptes rendus biologies.

[16]  Hiroyuki Ogata,et al.  AAindex: Amino Acid Index Database , 1999, Nucleic Acids Res..

[17]  On the formation of Asp‐tRNAAsn by aspartyl‐tRNA synthetases , 2005 .

[18]  F Wold,et al.  Posttranslational covalent modification of proteins. , 1977, Science.

[19]  Peter G Schultz,et al.  Adding amino acids to the genetic repertoire. , 2005, Current opinion in chemical biology.

[20]  R. W. Hall,et al.  Divergence, recombination and retention of functionality during protein evolution , 2005, Human Genomics.

[21]  Paul Schimmel,et al.  Incorporation of nonnatural amino acids into proteins. , 2004, Annual review of biochemistry.

[22]  N. Pace,et al.  The universal nature of biochemistry. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[23]  S. Pizzarello,et al.  Amino acids in meteorites. , 1983, Advances in space research : the official journal of the Committee on Space Research.

[24]  N. Grishin,et al.  Practical lessons from protein structure prediction , 2005, Nucleic acids research.

[25]  J P Doucet,et al.  Application of topological descriptors in QSAR and drug design: history and new trends. , 2002, Current drug targets. Infectious disorders.

[26]  Eörs Szathmáry,et al.  Why are there four letters in the genetic alphabet? , 2003, Nature Reviews Genetics.

[27]  Yan Zhang,et al.  Pyrrolysine and Selenocysteine Use Dissimilar Decoding Strategies* , 2005, Journal of Biological Chemistry.

[28]  J. Hailman.  Wonderful Life: The Burgess Shale and the Nature of History, Stephen Jay Gould. W. W. Norton, New York (1989), 347, Price $19.95 (U.S.A.), $27.95 (Canada) , 1991 .

[29]  Brian Hayes,et al.  THE INVENTION OF THE GENETIC CODE , 1998 .

[30]  Donald Hilvert,et al.  An Active Enzyme Constructed from a 9-Amino Acid Alphabet* , 2005, Journal of Biological Chemistry.

[31]  M. Berry,et al.  Unique features of selenocysteine incorporation function within the context of general eukaryotic translational processes. , 2005, Biochemical Society transactions.

[32]  P. Scholz,et al.  Chemical etiology of nucleic acid structure: the alpha-threofuranosyl-(3'-->2') oligonucleotide system. , 2000, Science.

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

[34]  László Orfi,et al.  Comparison of predictive ability of water solubility QSPR models generated by MLR, PLS and ANN methods. , 2004, Mini reviews in medicinal chemistry.

[35]  Eric J. Deeds,et al.  Protein structure and evolutionary history determine sequence space topology. , 2004, Genome research.

[36]  Peter Scholz,et al.  Chemical Etiology of Nucleic Acid Structure: The α-Threofuranosyl-(3'→2') Oligonucleotide System , 2000 .

[37]  Yovani Marrero Ponce,et al.  Linear indices of the 'macromolecular graph's nucleotides adjacency matrix' as a promising approach for bioinformatics studies. Part 1: prediction of paromomycin's affinity constant with HIV-1 psi-RNA packaging region. , 2005, Bioorganic & medicinal chemistry.

[38]  Richard A Goldstein,et al.  Why are proteins so robust to site mutations? , 2002, Journal of molecular biology.

[39]  Ron Elber,et al.  Enriching the sequence substitution matrix by structural information , 2003, Proteins.

[40]  E. Shock.  Astrobiology: Seeds of life? , 2002, Nature.

[41]  Eric Maréchal,et al.  Construction of non-symmetric substitution matrices derived from proteomes with biased amino acid distributions. , 2005, Comptes rendus biologies.

[42]  Stanley L. Miller,et al.  Reasons for the occurrence of the twenty coded protein amino acids , 1981, Journal of Molecular Evolution.

[43]  H D Dakin,et al.  On Amino-acids. , 1918, The Biochemical journal.

[44]  J. Prausnitz,et al.  Protein-folding landscapes in multichain systems. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[45]  Stephen F. Altschul,et al.  The construction of amino acid substitution matrices for the comparison of proteins with non-standard compositions , 2005, Bioinform..

[46]  Vadim N. Gladyshev,et al.  How Selenium Has Altered Our Understanding of the Genetic Code , 2002, Molecular and Cellular Biology.

[47]  M. O. Dayhoff,et al.  Atlas of protein sequence and structure , 1965 .

[48]  S. Miller.  Current status of the prebiotic synthesis of small molecules. , 1986, Chemica scripta.

[49]  S. Miller.  A production of amino acids under possible primitive earth conditions. , 1953, Science.

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