On the Uniqueness of the Standard Genetic Code

Zamudio, Gabriel S.; José, Marco V.

doi:10.3390/life7010007

Cited by 12 publications

(7 citation statements)

References 34 publications

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“…There are 4 x 10 84 possible genetic codes [55]. We used Hopfield networks to search for optimal genetic codes with the goal of assessing the possibility that SGC may have originated by a similar self-learning process.…”

Section: Resultsmentioning

confidence: 99%

Genetic codes optimized as a traveling salesman problem

Attie

Sulkow

et al. 2019

PLoS ONE

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The Standard Genetic Code (SGC) is robust to mutational errors such that frequently occurring mutations minimally alter the physio-chemistry of amino acids. The apparent correlation between the evolutionary distances among codons and the physio-chemical distances among their cognate amino acids suggests an early co-diversification between the codons and amino acids. Here we formulated the co-minimization of evolutionary distances between codons and physio-chemical distances between amino acids as a Traveling Salesman Problem (TSP) and solved it with a Hopfield neural network. In this unsupervised learning algorithm, macromolecules (e.g., tRNAs and aminoacyl-tRNA synthetases) associating codons with amino acids were considered biological analogs of Hopfield neurons associating “tour cities” with “tour positions”. The Hopfield network efficiently yielded an abundance of genetic codes that were more error-minimizing than SGC and could thus be used to design artificial genetic codes. We further argue that as a self-optimization algorithm, the Hopfield neural network provides a model of origin of SGC and other adaptive molecular systems through evolutionary learning.

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Section: Resultsmentioning

confidence: 99%

Genetic codes optimized as a traveling salesman problem

Attie

Sulkow

et al. 2019

PLoS ONE

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“…This calculation does not assume the evolution and degeneracy of the SGC. Coupling codon graphs of the SGC with different biological properties have allowed the analysis of several biological properties that uniquely determine the current SGC [29].…”

Section: Discussionmentioning

confidence: 99%

“…Codon graphs can be constructed for any subset of the 64 possible triplets. The RNY code has been modeled as a 4D hypercube [26,29,30]. Two genetic codes from which the primeval RNA code [25] could have originated the SGC have been derived [26].…”

Section: Methodsmentioning

confidence: 99%

“…The set of vertices of the quotient graph are the equivalent classes, and two vertices of the quotient graph are joined if there are elements of the equivalence classes that are joined in the original graph. The quotient graph derived from the codon graphs and a genetic code are known as phenotypic graphs [27][28][29][30]. The phenotypic graph represents the phenotypic expression of the codon hypercube; the vertices represent the 20 amino acids and the stop signal [22].…”

Section: Methodsmentioning

confidence: 99%

“…In the 6D hypercube, the vertices are indexed by the codons [13,26]. The hypercube of codons has been further transformed into its phenotypic graph representation [13,[28][29][30], where the new vertices are the amino acids and the stop signal.…”

Section: Introductionmentioning

confidence: 99%

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Symmetrical Properties of Graph Representations of Genetic Codes: From Genotype to Phenotype

José

Zamudio

2018

Symmetry

Self Cite

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It has long been claimed that the mitochondrial genetic code possesses more symmetries than the Standard Genetic Code (SGC). To test this claim, the symmetrical structure of the SGC is compared with noncanonical genetic codes. We analyzed the symmetries of the graphs of codons and their respective phenotypic graph representation spanned by the RNY (R purines, Y pyrimidines, and N any of them) code, two RNA Extended codes, the SGC, as well as three different mitochondrial genetic codes from yeast, invertebrates, and vertebrates. The symmetry groups of the SGC and their corresponding phenotypic graphs of amino acids expose the evolvability of the SGC. Indeed, the analyzed mitochondrial genetic codes are more symmetrical than the SGC.

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Origin of Life

Schulze‐Makuch¹,

Irwin²

2018

Life in the Universe

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On the Uniqueness of the Standard Genetic Code

Cited by 12 publications

References 34 publications

Genetic codes optimized as a traveling salesman problem

Genetic codes optimized as a traveling salesman problem

Symmetrical Properties of Graph Representations of Genetic Codes: From Genotype to Phenotype

Origin of Life

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