ArticleProceedings of the National Academy of Sciences of the United States of America2000
Testing a biosynthetic theory of the genetic code: fact or artifact?
Article in Proceedings of the National Academy of Sciences of the United States of America, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Fitting the standard genetic code into its triplet table.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Evolution of the Standard Genetic Code.Journal of molecular evolution · 2021Article
- Optimal Evolution of the Standard Genetic Code.Journal of molecular evolution · 2021Article
- Genetic code and metabolism: The perpetual waltz.The Journal of biological chemistry · 2018Article
- Optimization of the standard genetic code according to three codon positions using an evolutionary algorithm.PloS one · 2018Article
- An integrated, structure- and energy-based view of the genetic code.Nucleic acids research · 2016Review
- Origins of tmRNA: the missing link in the birth of protein synthesis?Nucleic acids research · 2016Review
- From the primordial soup to self-driving cars: standards and their role in natural and technological innovation.Journal of the Royal Society, Interface · 2016Review
- Pathways of Genetic Code Evolution in Ancient and Modern Organisms.Journal of molecular evolution · 2015Review
- Ancestral AlaX editing enzymes for control of genetic code fidelity are not tRNA-specific.The Journal of biological chemistry · 2015Article
- Genetic code evolution started with the incorporation of glycine, followed by other small hydrophilic amino acids.Journal of molecular evolution · 2014Article
- Imprints of the genetic code in the ribosome.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Origin and evolution of the genetic code: the universal enigma.IUBMB life · 2009Review
- An extension of the coevolution theory of the origin of the genetic code.Biology direct · 2008Article
- Evolutionary patterns in the sequence and structure of transfer RNA: a window into early translation and the genetic code.PloS one · 2008Article
- Transfer RNA and the origins of diversified life.Science progress · 2008Review
- A content-centric organization of the genetic code.Genomics, proteomics & bioinformatics · 2007Article
- Error minimization and coding triplet/binding site associations are independent features of the canonical genetic code.Journal of molecular evolution · 2005Article
- On the structural regularity in nucleobases and amino acids and relationship to the origin and evolution of the genetic code.Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life · 2005Article
- A new classification scheme of the genetic code.Journal of molecular evolution · 2004Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
It has long been conjectured that the canonical genetic code evolved from a simpler primordial form that encoded fewer amino acids [e.g., Crick, F. H. C. (1968) J. Mol. Biol. 38, 367-379]. The most influential form of this idea, "code coevolution" [Wong, J. T.-F. (1975) Proc. Natl. Acad. Sci. USA 72, 1909-1912], proposes that the genetic code coevolved with the invention of biosynthetic pathways for new amino acids. It further proposes that a comparison of modern codon assignments with the conserved metabolic pathways of amino acid biosynthesis can inform us about this history of code expansion. Here we re-examine the biochemical basis of this theory to test the validity of its statistical support. We show that the theory's definition of "precursor-product" amino acid pairs is unjustified biochemically because it requires the energetically unfavorable reversal of steps in extant metabolic pathways to achieve desired relationships. In addition, the theory neglects important biochemical constraints when calculating the probability that chance could assign precursor-product amino acids to contiguous codons. A conservative correction for these errors reveals a surprisingly high 23% probability that apparent patterns within the code are caused purely by chance. Finally, even this figure rests on post hoc assumptions about primordial codon assignments, without which the probability rises to 62% that chance alone could explain the precursor-product pairings found within the code. Thus we conclude that coevolution theory cannot adequately explain the structure of the genetic code.
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