Dihedral Group in The Ancient Genetic

The standard genetic code consist of four nucleotide bases which encode genes to produce amino acids needed by living things. The addition of new base (Dummy) causes a sequence of bases to become five nucleotide bases called ancient genetic codes. The five base set is denoted by , where B forms group through matching , , , , and from set . Ancient genetic codes can be reviewed as algebraic structures as a vector spaces and other structures as symmetry groups. In this article, discussed the properties of symmetry groups from ancient genetic codes that will produce dihedral groups. The study began by constructing an expanded nucleotide base isomorphism with . The presence of base causes to have a cardinality of 24, denoted as with . isomorphic with which is denoted by . Group had three clasess of partitions based on strong-weak, purin-pyrimidin types, and amino-keto nucleotide groups which are denoted as , , and . All three classes are subgroups of . By using the rules of rotation and reflection in the four-side plane, it was found that only one group fulfilled the rule was named the dihedral group. Keywords: ancient genetic code, group, subgroup, permutation, symmetry group , dihedral group.

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

Symmetry ◽

10.3390/sym10090388 ◽

2018 ◽

Vol 10 (9) ◽

pp. 388 ◽

Cited By ~ 2

Author(s):

Marco José ◽

Gabriel Zamudio

Keyword(s):

Amino Acids ◽

Genetic Code ◽

Graph Representation ◽

Symmetry Groups ◽

Standard Genetic Code ◽

Graph Representations ◽

Symmetrical Structure ◽

Genetic Codes ◽

Mitochondrial Genetic Code

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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On the Importance of Asymmetry in the Phenotypic Expression of the Genetic Code upon the Molecular Evolution of Proteins

Symmetry ◽

10.3390/sym12060997 ◽

2020 ◽

Vol 12 (6) ◽

pp. 997

Author(s):

Marco V. José ◽

Gabriel S. Zamudio

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Genetic Code ◽

Phenotypic Expression ◽

Standard Genetic Code ◽

Specific Amino Acid ◽

Trna Synthetases ◽

Probability Of Occurrence ◽

Genetic Codes ◽

Evolution Of Proteins

The standard genetic code (SGC) is a mapping between the 64 possible arrangements of the four RNA nucleotides (C, A, U, G) into triplets or codons, where 61 codons are assigned to a specific amino acid and the other three are stop codons for terminating protein synthesis. Aminoacyl-tRNA synthetases (aaRSs) are responsible for implementing the SGC by specifically amino-acylating only its cognate transfer RNA (tRNA), thereby linking an amino acid with its corresponding anticodon triplets. tRNAs molecules bind each codon with its anticodon. To understand the meaning of symmetrical/asymmetrical properties of the SGC, we designed synthetic genetic codes with known symmetries and with the same degeneracy of the SGC. We determined their impact on the substitution rates for each amino acid under a neutral model of protein evolution. We prove that the phenotypic graphs of the SGC for codons and anticodons for all the possible arrangements of nucleotides are asymmetric and the amino acids do not form orbits. In the symmetrical synthetic codes, the amino acids are grouped according to their codonicity, this is the number of triplets encoding a given amino acid. Both the SGC and symmetrical synthetic codes exhibit a probability of occurrence of the amino acids proportional to their degeneracy. Unlike the SGC, the synthetic codes display a constant probability of occurrence of the amino acid according to their codonicity. The asymmetry of the phenotypic graphs of codons and anticodons of the SGC, has important implications on the evolutionary processes of proteins.

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Optimization of Expanded Genetic Codes via Genetic Algorithms

10.5753/eniac.2018.4440 ◽

2018 ◽

Author(s):

Maísa de Carvalho Silva ◽

Lariza Laura De Oliveira ◽

Renato Tinós

Keyword(s):

Amino Acids ◽

Genetic Algorithms ◽

Amino Acid ◽

Genetic Code ◽

Unnatural Amino Acids ◽

Genetically Modified Organisms ◽

Fitness Function ◽

Unnatural Amino Acid ◽

Standard Genetic Code ◽

Genetic Codes

In the last decades, researchers have proposed the use of genetically modified organisms that utilize unnatural amino acids, i.e., amino acids other than the 20 amino acids encoded in the standard genetic code. Unnatural amino acids have been incorporated into genetically engineered organisms for the development of new drugs, fuels and chemicals. When new amino acids are incorporated, it is necessary to modify the standard genetic code. Expanded genetic codes have been created without considering the robustness of the code. The objective of this work is the use of genetic algorithms (GAs) for the optimization of expanded genetic codes. The GA indicates which codons of the standard genetic code should be used to encode a new unnatural amino acid. The fitness function has two terms; one for robustness of the new code and another that takes into account the frequency of use of amino acids. Experiments show that, by controlling the weighting between the two terms, it is possible to obtain more or less amino acid substitutions at the same time that the robustness is minimized.

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A working hypothesis on the interdependent genesis of nucleotide bases, protein amino acids, and primitive genetic code

Origins of Life ◽

10.1007/bf00931385 ◽

1981 ◽

Vol 11 (3) ◽

pp. 197-202 ◽

Cited By ~ 7

Author(s):

Fujio Egami

Keyword(s):

Amino Acids ◽

Genetic Code ◽

Working Hypothesis ◽

Protein Amino Acids ◽

Nucleotide Bases

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Some theoretical aspects of reprogramming the standard genetic code

10.1101/2020.09.12.294553 ◽

2020 ◽

Author(s):

Kuba Nowak ◽

Paweł Błażej ◽

Małgorzata Wnetrzak ◽

Dorota Mackiewicz ◽

Paweł Mackiewicz

Keyword(s):

Amino Acids ◽

Genetic Code ◽

Dna Sequences ◽

Theoretical Perspective ◽

Optimal Number ◽

Optimal Size ◽

Coding System ◽

Standard Genetic Code ◽

Nucleotide Mutation ◽

Code Extension

1AbstractReprogramming of the standard genetic code in order to include non-canonical amino acids (ncAAs) opens a new perspective in medicine, industry and biotechnology. There are several methods of engineering the code, which allow us for storing new genetic information in DNA sequences and transmitting it into the protein world. Here, we investigate the problem of optimal genetic code extension from theoretical perspective. We assume that the new coding system should encode both canonical and new ncAAs using 64 classical codons. What is more, the extended genetic code should be robust to point nucleotide mutation and minimize the possibility of reversion from new to old information. In order to do so, we follow graph theory to study the properties of optimal codon sets, which can encode 20 canonical amino acids and stop coding signal. Finally, we describe the set of vacant codons that could be assigned to new amino acids. Moreover, we discuss the optimal number of the newly incorporated ncAAs and also the optimal size of codon blocks that are assigned to ncAAs.

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Golden and Harmonic Mean in the Genetic Code

10.31219/osf.io/2pfe7 ◽

2017 ◽

Author(s):

Miloje M. Rakocevic

Keyword(s):

Amino Acids ◽

Genetic Code ◽

Harmonic Mean ◽

Standard Genetic Code ◽

Code Table ◽

Nucleotide Triplet

In previous two works [1], [2] we have shown the determination of genetic code by golden and harmonic mean within standard Genetic Code Table, i.e. nucleotide triplet table, whereas in this paper we show the same determination through a specific connection between two tables – of nucleotide doublets Table and triplets Table, over polarity of amino acids, measured by Cloister energy.

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Did Amino Acid Side Chain Reactivity Dictate the Composition and Timing of Aminoacyl-tRNA Synthetase Evolution?

Genes ◽

10.3390/genes12030409 ◽

2021 ◽

Vol 12 (3) ◽

pp. 409

Author(s):

Tamara L. Hendrickson ◽

Whitney N. Wood ◽

Udumbara M. Rathnayake

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Genetic Code ◽

Chemical Reactivity ◽

Trna Synthetase ◽

Amino Acid Side Chain ◽

Standard Genetic Code ◽

Last Universal Common Ancestor ◽

Trna Synthetases ◽

Universal Common Ancestor

The twenty amino acids in the standard genetic code were fixed prior to the last universal common ancestor (LUCA). Factors that guided this selection included establishment of pathways for their metabolic synthesis and the concomitant fixation of substrate specificities in the emerging aminoacyl-tRNA synthetases (aaRSs). In this conceptual paper, we propose that the chemical reactivity of some amino acid side chains (e.g., lysine, cysteine, homocysteine, ornithine, homoserine, and selenocysteine) delayed or prohibited the emergence of the corresponding aaRSs and helped define the amino acids in the standard genetic code. We also consider the possibility that amino acid chemistry delayed the emergence of the glutaminyl- and asparaginyl-tRNA synthetases, neither of which are ubiquitous in extant organisms. We argue that fundamental chemical principles played critical roles in fixation of some aspects of the genetic code pre- and post-LUCA.

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Many alternative and theoretical genetic codes are more robust to amino acid replacements than the standard genetic code

Journal of Theoretical Biology ◽

10.1016/j.jtbi.2018.12.030 ◽

2019 ◽

Vol 464 ◽

pp. 21-32 ◽

Cited By ~ 11

Author(s):

Paweł Błażej ◽

Małgorzata Wnętrzak ◽

Dorota Mackiewicz ◽

Przemysław Gagat ◽

Paweł Mackiewicz

Keyword(s):

Amino Acid ◽

Genetic Code ◽

Standard Genetic Code ◽

Genetic Codes

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Golden and Harmonic Mean in the Genetic Code

10.31219/osf.io/fzgjp ◽

2017 ◽

Author(s):

Miloje M. Rakocevic

Keyword(s):

Amino Acids ◽

Genetic Code ◽

Harmonic Mean ◽

Standard Genetic Code ◽

International Conference ◽

Theoretical Approaches ◽

Code Table ◽

Nucleotide Triplet ◽

Polar Requirement

In previous two works (Rakočević, 1998; 2013), we have shown the determination of genetic code by golden and harmonic mean within standard Genetic Code Table, i.e. nucleotide triplet table, whereas in this paper we show the same determination through a specific connection between two tables – of nucleotide doublets Table and triplets Table, over polarity of amino acids, measured by Cloister energy in general, and by hydropathy and polar requirement, partialy. [This is the expanded version of the article published in Proceedings of the 2nd International Conference “Theoretical Approaches to BioInformation Systems” (TABIS.2013), September 17–22, 2013, Belgrade, Serbia. That first version is also stored, as Version 1, in OSF Preprints.]

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