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1

Di Giulio, Massimo. "The genetic code is not universal." BioSystems 247 (January 2025): 105382. https://doi.org/10.1016/j.biosystems.2024.105382.

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2

shCherbak, Vladimir I. "Arithmetic inside the universal genetic code." Biosystems 70, no. 3 (2003): 187–209. http://dx.doi.org/10.1016/s0303-2647(03)00066-2.

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3

Suzuki, Takeo, Kenjyo Miyauchi, Tsutomu Suzuki, et al. "Taurine-containing Uridine Modifications in tRNA Anticodons Are Required to Decipher Non-universal Genetic Codes in Ascidian Mitochondria." Journal of Biological Chemistry 286, no. 41 (2011): 35494–98. http://dx.doi.org/10.1074/jbc.m111.279810.

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Variations in the genetic code are found frequently in mitochondrial decoding systems. Four non-universal genetic codes are employed in ascidian mitochondria: AUA for Met, UGA for Trp, and AGA/AGG(AGR) for Gly. To clarify the decoding mechanism for the non-universal genetic codes, we isolated and analyzed mitochondrial tRNAs for Trp, Met, and Gly from an ascidian, Halocynthia roretzi. Mass spectrometric analysis identified 5-taurinomethyluridine (τm5U) at the anticodon wobble positions of tRNAMet(AUR), tRNATrp(UGR), and tRNAGly(AGR), suggesting that τm5U plays a critical role in the accurate deciphering of all four non-universal codes by preventing the misreading of pyrimidine-ending near-cognate codons (NNY) in their respective family boxes. Acquisition of the wobble modification appears to be a prerequisite for the genetic code alteration.
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4

H., Pawlowski Piotr. "The Smooth Evolution of the Universal Genetic Code. Main Episodes." International Journal of Sciences Volume 8, no. 2019-09 (2019): 28–51. https://doi.org/10.5281/zenodo.3979985.

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The possible scenario of the origin and evolution of genetic code is proposed, being primarily implicated by the working hypothesis which states that the chronological order of amino acids evolutionary implementation monotonically correlates with their increasing mass. It fulfills the minimalistic claim of the smallest changes of the evolving system at increasing complexity, hereinafter called "the smooth evolution". The working hypothesis was postulated concerning the results of statistical analysis indicating a strong correlation between amino acid mass and the chosen parameters of contemporary genetic code, which are expected to change in a certain individual direction during the evolution of the initial genetic system. It was additionally supplemented by the most common hypotheses adopted from the literature, as stereochemical, 'frozen accident' and coevolutional. The developed scenario allows a detailed description of the twenty-two consecutive episodes of the history of code definition and the estimation of its dynamics. It reveals the main eras of evolution conditioned by the environmental and structural constraints. It also lets the estimation of the evolutionary frequencies of codon sense expansion, and redefinition. Dominating trends and amino acids were indicated. The underlying assumptions, limits, exceptions, and the future of the code evolution have been discussed.Read Complete Article at ijSciences: V82019092180 AND DOI: http://dx.doi.org/10.18483/ijSci.2180
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5

Kück, Ulrich, and Heike Neuhaus. "Universal genetic code evidenced in mitochondria ofChlamydomonas reinhardii." Applied Microbiology and Biotechnology 23, no. 6 (1986): 462–69. http://dx.doi.org/10.1007/bf02346061.

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6

Koonin, Eugene V., and Artem S. Novozhilov. "Origin and Evolution of the Universal Genetic Code." Annual Review of Genetics 51, no. 1 (2017): 45–62. http://dx.doi.org/10.1146/annurev-genet-120116-024713.

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7

Ishigami, Masahiro, Hideshi Ihara, and Hiroyuki Shinoda. "Molecular Evolution of Aminoacyl tRNA Synthetases and Origin of Universal Genetic Code." International Astronomical Union Colloquium 161 (January 1997): 483–89. http://dx.doi.org/10.1017/s0252921100015013.

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AbstractIt is thought that living things first appeared on the primitive earth 35 hundred million years ago. At that time, a primitive protein synthesis mechanism was thought to have been established, a genetic code system evolved, and a universal genetic code system developed. Aminoacyl tRNA synthetase must have evolved with the genetic code system. The aim of the present study is to clarify the evolution of aminoacyl tRNA synthetase and the process and era of the establishment of the universal genetic code system.
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8

Omachi, Yuji, Nen Saito, and Chikara Furusawa. "Rare-event sampling analysis uncovers the fitness landscape of the genetic code." PLOS Computational Biology 19, no. 4 (2023): e1011034. http://dx.doi.org/10.1371/journal.pcbi.1011034.

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The genetic code refers to a rule that maps 64 codons to 20 amino acids. Nearly all organisms, with few exceptions, share the same genetic code, the standard genetic code (SGC). While it remains unclear why this universal code has arisen and been maintained during evolution, it may have been preserved under selection pressure. Theoretical studies comparing the SGC and numerically created hypothetical random genetic codes have suggested that the SGC has been subject to strong selection pressure for being robust against translation errors. However, these prior studies have searched for random genetic codes in only a small subspace of the possible code space due to limitations in computation time. Thus, how the genetic code has evolved, and the characteristics of the genetic code fitness landscape, remain unclear. By applying multicanonical Monte Carlo, an efficient rare-event sampling method, we efficiently sampled random codes from a much broader random ensemble of genetic codes than in previous studies, estimating that only one out of every 1020 random codes is more robust than the SGC. This estimate is significantly smaller than the previous estimate, one in a million. We also characterized the fitness landscape of the genetic code that has four major fitness peaks, one of which includes the SGC. Furthermore, genetic algorithm analysis revealed that evolution under such a multi-peaked fitness landscape could be strongly biased toward a narrow peak, in an evolutionary path-dependent manner.
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9

Yarus, Michael. "Optimal Evolution of the Standard Genetic Code." Journal of Molecular Evolution 89, no. 1-2 (2021): 45–49. http://dx.doi.org/10.1007/s00239-020-09984-8.

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AbstractThe Standard Genetic Code (SGC) exists in every known organism on Earth. SGC evolution via early unique codon assignment, then later wobble, yields coding resembling the near-universal code. Below, later wobble is shown to also create an optimal route to accurate codon assignment. Time of optimal codon assignment matches the previously defined mean time for ordered coding, exhibiting ≥ 90% of SGC order. Accurate evolution is also accessible, sufficiently frequent to appear in populations of 103 to 104 codes. SGC-like coding capacity, code order, and accurate assignments therefore arise together, in one attainable evolutionary intermediate. Examples, which plausibly resemble coding at evolutionary domain separation, are characterized.
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10

Rosenberg, Roger N. "The universal brain code a genetic mechanism for memory." Journal of the Neurological Sciences 429 (October 2021): 118073. http://dx.doi.org/10.1016/j.jns.2021.118073.

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11

Lukashenko, N. P. "Evolutionary deviations from the universal genetic code in ciliates." Russian Journal of Genetics 45, no. 4 (2009): 379–88. http://dx.doi.org/10.1134/s1022795409040012.

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12

Hatfield, Dolph, and Alan Diamond. "UGA: A split personality in the universal genetic code." Trends in Genetics 9, no. 3 (1993): 69–70. http://dx.doi.org/10.1016/0168-9525(93)90215-4.

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13

Parker, J. "Errors and alternatives in reading the universal genetic code." Microbiological Reviews 53, no. 3 (1989): 273–98. http://dx.doi.org/10.1128/mmbr.53.3.273-298.1989.

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14

Parker, J. "Errors and alternatives in reading the universal genetic code." Microbiological Reviews 53, no. 3 (1989): 273–98. http://dx.doi.org/10.1128/mr.53.3.273-298.1989.

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15

Gonzalez, D. L., S. Giannerini, and R. Rosa. "On the origin of degeneracy in the genetic code." Interface Focus 9, no. 6 (2019): 20190038. http://dx.doi.org/10.1098/rsfs.2019.0038.

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The degeneracy of amino acid coding is one of the most crucial and enigmatic aspects of the genetic code. Different theories about the origin of the genetic code have been developed. However, to date, there is no comprehensive hypothesis on the mechanism that might have generated the degeneracy as we observe it. Here, we provide a new theory that explains the origin of the degeneracy based only on symmetry principles. The approach allows one to describe exactly the degeneracy of the early code (progenitor of the genetic code of LUCA, the last universal common ancestor) which is hypothesized to have the same degeneracy as the present vertebrate mitochondrial genetic code. The theory is based upon the tessera code, that fits as the progenitor of the early code. Moreover, we describe in detail the possible evolutionary transitions implied by our theory. The approach is supported by a unified mathematical framework that accounts for the degeneracy properties of both nuclear and mitochondrial genetic codes. Our work provides a new perspective to the understanding of the origin of the genetic code and the roles of symmetry principles in the organization of genetic information.
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16

Pesole, G., M. Lotti, L. Alberghina, and C. Saccone. "Evolutionary origin of nonuniversal CUGSer codon in some Candida species as inferred from a molecular phylogeny." Genetics 141, no. 3 (1995): 903–7. http://dx.doi.org/10.1093/genetics/141.3.903.

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Abstract CUG, a universal leucine codon, has been reported to be read as serine in various yeast species belonging to the genus Candida. To gain a deeper insight into the origin of this deviation from the universal genetic code, we carried out a phylogenetic analysis based on the small-subunit ribosomal RNA genes from some Candida and other related Hemiascomycetes. Furthermore, we determined the phylogenetic relationships between the tRNA(Ser)CAG, responsible for the translation of CUG, from some Candida species and the other serine and leucine isoacceptor tRNAs in C. cylindracea. We demonstrate that the group of Candida showing the genetic code deviation is monophyletic and that this deviation could have originated more than 150 million years ago. We also describe how phylogenetic analysis can be used for genetic code predictions.
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17

Szymański, Maciej, and Jan Barciszewski. "The genetic code--40 years on." Acta Biochimica Polonica 54, no. 1 (2007): 51–54. http://dx.doi.org/10.18388/abp.2007_3268.

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The genetic code discovered 40 years ago, consists of 64 triplets (codons) of nucleotides. The genetic code is almost universal. The same codons are assigned to the same amino acids and to the same START and STOP signals in the vast majority of genes in animals, plants, and microorganisms. Each codon encodes for one of the 20 amino acids used in the synthesis of proteins. That produces some redundancy in the code and most of the amino acids being encoded by more than one codon. The two cases have been found where selenocysteine or pyrrolysine, that are not one of the standard 20 is inserted by a tRNA into the growing polypeptide.
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18

H. Pawlowski, Piotr. "The Smooth Evolution of the Universal Genetic Code. Main Episodes." International Journal of Sciences 8, no. 09 (2019): 28–51. http://dx.doi.org/10.18483/ijsci.2180.

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19

Zhaksybayeva, Olga A. "Statistical estimation of rumer's transformation of the universal genetic code." Origins of Life and Evolution of the Biosphere 26, no. 3-5 (1996): 444–45. http://dx.doi.org/10.1007/bf02459859.

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20

Koonin, Eugene V., and Artem S. Novozhilov. "Origin and evolution of the genetic code: The universal enigma." IUBMB Life 61, no. 2 (2009): 99–111. http://dx.doi.org/10.1002/iub.146.

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21

Koonin, Eugene V., and Artem S. Novozhilov. "Origin and evolution of the genetic code: The universal enigma." IUBMB Life 61, no. 2 (2009): spcone. http://dx.doi.org/10.1002/iub.190.

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22

Diwo, Christian, and Nediljko Budisa. "Alternative Biochemistries for Alien Life: Basic Concepts and Requirements for the Design of a Robust Biocontainment System in Genetic Isolation." Genes 10, no. 1 (2018): 17. http://dx.doi.org/10.3390/genes10010017.

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The universal genetic code, which is the foundation of cellular organization for almost all organisms, has fostered the exchange of genetic information from very different paths of evolution. The result of this communication network of potentially beneficial traits can be observed as modern biodiversity. Today, the genetic modification techniques of synthetic biology allow for the design of specialized organisms and their employment as tools, creating an artificial biodiversity based on the same universal genetic code. As there is no natural barrier towards the proliferation of genetic information which confers an advantage for a certain species, the naturally evolved genetic pool could be irreversibly altered if modified genetic information is exchanged. We argue that an alien genetic code which is incompatible with nature is likely to assure the inhibition of all mechanisms of genetic information transfer in an open environment. The two conceivable routes to synthetic life are either de novo cellular design or the successive alienation of a complex biological organism through laboratory evolution. Here, we present the strategies that have been utilized to fundamentally alter the genetic code in its decoding rules or its molecular representation and anticipate future avenues in the pursuit of robust biocontainment.
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23

Palacios-Pérez, Miryam, and Marco V. José. "A Proposal for the RNAome at the Dawn of the Last Universal Common Ancestor." Genes 15, no. 9 (2024): 1195. http://dx.doi.org/10.3390/genes15091195.

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From the most ancient RNAs, which followed an RNY pattern and folded into small hairpins, modern RNA molecules evolved by two different pathways, dubbed Extended Genetic Code 1 and 2, finally conforming to the current standard genetic code. Herein, we describe the evolutionary path of the RNAome based on these evolutionary routes. In general, all the RNA molecules analysed contain portions encoded by both genetic codes, but crucial features seem to be better recovered by Extended 2 triplets. In particular, the whole Peptidyl Transferase Centre, anti-Shine–Dalgarno motif, and a characteristic quadruplet of the RNA moiety of RNAse-P are clearly unveiled. Differences between bacteria and archaea are also detected; in most cases, the biological sequences are more stable than their controls. We then describe an evolutionary trajectory of the RNAome formation, based on two complementary evolutionary routes: one leading to the formation of essentials, while the other complemented the molecules, with the cooperative assembly of their constituents giving rise to modern RNAs.
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24

Arranz-Gibert, Pol, Jaymin R. Patel, and Farren J. Isaacs. "The Role of Orthogonality in Genetic Code Expansion." Life 9, no. 3 (2019): 58. http://dx.doi.org/10.3390/life9030058.

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The genetic code defines how information in the genome is translated into protein. Aside from a handful of isolated exceptions, this code is universal. Researchers have developed techniques to artificially expand the genetic code, repurposing codons and translational machinery to incorporate nonstandard amino acids (nsAAs) into proteins. A key challenge for robust genetic code expansion is orthogonality; the engineered machinery used to introduce nsAAs into proteins must co-exist with native translation and gene expression without cross-reactivity or pleiotropy. The issue of orthogonality manifests at several levels, including those of codons, ribosomes, aminoacyl-tRNA synthetases, tRNAs, and elongation factors. In this concept paper, we describe advances in genome recoding, translational engineering and associated challenges rooted in establishing orthogonality needed to expand the genetic code.
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25

Ibba, M., A. W. Curnow, J. Bono, P. A. Rosa, C. R. Woese, and D. Söll. "Archaeal Aminoacyl-tRNA Synthesis: Unique Determinants of a Universal Genetic Code?" Biological Bulletin 196, no. 3 (1999): 335–37. http://dx.doi.org/10.2307/1542964.

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26

Hohn, M. J., H. S. Park, P. O'Donoghue, M. Schnitzbauer, and D. Soll. "Emergence of the universal genetic code imprinted in an RNA record." Proceedings of the National Academy of Sciences 103, no. 48 (2006): 18095–100. http://dx.doi.org/10.1073/pnas.0608762103.

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27

Yarus, Michael. "Evolution of the Standard Genetic Code." Journal of Molecular Evolution 89, no. 1-2 (2021): 19–44. http://dx.doi.org/10.1007/s00239-020-09983-9.

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AbstractA near-universal Standard Genetic Code (SGC) implies a single origin for present Earth life. To study this unique event, I compute paths to the SGC, comparing different plausible histories. Notably, SGC-like coding emerges from traditional evolutionary mechanisms, and a superior route can be identified. To objectively measure evolution, progress values from 0 (random coding) to 1 (SGC-like) are defined: these measure fractions of random-code-to-SGC distance. Progress types are spacing/distance/delta Polar Requirement, detecting space between identical assignments/mutational distance to the SGC/chemical order, respectively. The coding system is based on selected RNAs performing aminoacyl-RNA synthetase reactions. Acceptor RNAs exhibit SGC-like Crick wobble; alternatively, non-wobbling triplets uniquely encode 20 amino acids/start/stop. Triplets acquire 22 functions by stereochemistry, selection, coevolution, or at random. Assignments also propagate to an assigned triplet’s neighborhood via single mutations, but can also decay. A vast code universe makes futile evolutionary paths plentiful. Thus, SGC evolution is critically sensitive to disorder from random assignments. Evolution also inevitably slows near coding completion. The SGC likely avoided these difficulties, and two suitable paths are compared. In late wobble, a majority of non-wobble assignments are made before wobble is adopted. In continuous wobble, a uniquely advantageous early intermediate yields an ordered SGC. Revised coding evolution (limited randomness, late wobble, concentration on amino acid encoding, chemically conservative coevolution with a chemically ordered elite) produces varied full codes with excellent joint progress values. A population of only 600 independent coding tables includes SGC-like members; a Bayesian path toward more accurate SGC evolution is available.
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28

Makukov, Maxim A., and Vladimir I. shCherbak. "SETIin vivo: testing the we-are-them hypothesis." International Journal of Astrobiology 17, no. 2 (2017): 127–46. http://dx.doi.org/10.1017/s1473550417000210.

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AbstractAfter it was proposed that life on Earth might descend from seeding by an earlier extraterrestrial civilization motivated to secure and spread life, some authors noted that this alternative offers a testable implication: microbial seeds could be intentionally supplied with a durable signature that might be found in extant organisms. In particular, it was suggested that the optimal location for such an artefact is the genetic code, as the least evolving part of cells. However, as the mainstream view goes, this scenario is too speculative and cannot be meaningfully tested because encoding/decoding a signature within the genetic code is something ill-defined, so any retrieval attempt is doomed to guesswork. Here we refresh the seeded-Earth hypothesis in light of recent observations, and discuss the motivation for inserting a signature. We then show that ‘biological SETI’ involves even weaker assumptions than traditional SETI and admits a well-defined methodological framework. After assessing the possibility in terms of molecular and evolutionary biology, we formalize the approach and, adopting the standard guideline of SETI that encoding/decoding should follow from first principles and be convention-free, develop a universal retrieval strategy. Applied to the canonical genetic code, it reveals a non-trivial precision structure of interlocked logical and numerical attributes of systematic character (previously we found these heuristically). To assess this result in view of the initial assumption, we perform statistical, comparison, interdependence and semiotic analyses. Statistical analysis reveals no causal connection of the result to evolutionary models of the genetic code, interdependence analysis precludes overinterpretation, and comparison analysis shows that known variations of the code lack any precision-logic structures, in agreement with these variations being post-LUCA (i.e. post-seeding) evolutionary deviations from the canonical code. Finally, semiotic analysis shows that not only the found attributes are consistent with the initial assumption, but that they make perfect sense from SETI perspective, as they ultimately maintain some of the most universal codes of culture.
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29

Verkhovod, A. B. "Alphanumerical Divisions of the Universal Genetic Code: New Divisions Reveal New Balances." Journal of Theoretical Biology 170, no. 3 (1994): 327–30. http://dx.doi.org/10.1006/jtbi.1994.1194.

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30

McGowan, Jamie, Estelle S. Kilias, Elisabet Alacid, et al. "Identification of a non-canonical ciliate nuclear genetic code where UAA and UAG code for different amino acids." PLOS Genetics 19, no. 10 (2023): e1010913. http://dx.doi.org/10.1371/journal.pgen.1010913.

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The genetic code is one of the most highly conserved features across life. Only a few lineages have deviated from the “universal” genetic code. Amongst the few variants of the genetic code reported to date, the codons UAA and UAG virtually always have the same translation, suggesting that their evolution is coupled. Here, we report the genome and transcriptome sequencing of a novel uncultured ciliate, belonging to the Oligohymenophorea class, where the translation of the UAA and UAG stop codons have changed to specify different amino acids. Genomic and transcriptomic analyses revealed that UAA has been reassigned to encode lysine, while UAG has been reassigned to encode glutamic acid. We identified multiple suppressor tRNA genes with anticodons complementary to the reassigned codons. We show that the retained UGA stop codon is enriched in the 3’UTR immediately downstream of the coding region of genes, suggesting that there is functional drive to maintain tandem stop codons. Using a phylogenomics approach, we reconstructed the ciliate phylogeny and mapped genetic code changes, highlighting the remarkable number of independent genetic code changes within the Ciliophora group of protists. According to our knowledge, this is the first report of a genetic code variant where UAA and UAG encode different amino acids.
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31

Kawakami, Takashi, and Hiroshi Murakami. "Genetically Encoded Libraries of Nonstandard Peptides." Journal of Nucleic Acids 2012 (2012): 1–15. http://dx.doi.org/10.1155/2012/713510.

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The presence of a nonproteinogenic moiety in a nonstandard peptide often improves the biological properties of the peptide. Non-standard peptide libraries are therefore used to obtain valuable molecules for biological, therapeutic, and diagnostic applications. Highly diverse non-standard peptide libraries can be generated by chemically or enzymatically modifying standard peptide libraries synthesized by the ribosomal machinery, using posttranslational modifications. Alternatively, strategies for encoding non-proteinogenic amino acids into the genetic code have been developed for the direct ribosomal synthesis of non-standard peptide libraries. In the strategies for genetic code expansion, non-proteinogenic amino acids are assigned to the nonsense codons or 4-base codons in order to add these amino acids to the universal genetic code. In contrast, in the strategies for genetic code reprogramming, some proteinogenic amino acids are erased from the genetic code and non-proteinogenic amino acids are reassigned to the blank codons. Here, we discuss the generation of genetically encoded non-standard peptide libraries using these strategies and also review recent applications of these libraries to the selection of functional non-standard peptides.
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32

Döring, Volker, and Philippe Marlière. "Reassigning Cysteine in the Genetic Code of Escherichia coli." Genetics 150, no. 2 (1998): 543–51. http://dx.doi.org/10.1093/genetics/150.2.543.

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Abstract We investigated directed deviations from the universal genetic code. Mutant tRNAs that incorporate cysteine at positions corresponding to the isoleucine AUU, AUC, and AUA and methionine AUG codons were introduced in Escherichia coli K12. Missense mutations at the cysteine catalytic site of thymidylate synthase were systematically crossed with synthetic suppressor tRNACys genes coexpressed from compatible plasmids. Strains harboring complementary codon/anticodon associations could be stably propagated as thymidine prototrophs. A plasmid-encoded tRNACys reading the codon AUA persisted for more than 500 generations in a strain requiring its suppressor activity for thymidylate biosynthesis, but was eliminated from a strain not requiring it. Cysteine miscoding at the codon AUA was also enforced in the active site of amidase, an enzyme found in Helicobacter pylori and not present in wild-type E. coli. Propagating the amidase missense mutation in E. coli with an aliphatic amide as nitrogen source required the overproduction of Cys-tRNA synthetase together with the complementary suppressor tRNACys. The toxicity of cysteine miscoding was low in all our strains. The small size and amphiphilic character of this amino acid may render it acceptable as a replacement at most protein positions and thus apt to overcome the steric and polar constraints that limit evolution of the genetic code.
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33

Kayumov, A. R., AA A. Saetgaraeva, OA A. Markelov, and M. I. Bogachev. "Statistical laws of eukaryotic DNA patchiness." Genes & Cells 9, no. 3 (2014): 89–93. http://dx.doi.org/10.23868/gc120321.

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Active development of the genetic engineering and expression of foreign genes in various organisms revealed the requirement of the DNA sequences adaptation to the genetic machinery of a host cell including adaptation of both functional elements of the genetic code and its tertiary architecture. The annotated genomes of organisms at different evolutionary levels that are widely used as models were obtained from the Genbank (ftp://ftp.ncbi.nlm.nih.gov/genomes). The probability density functions of the sizes of structural elements of the genetic code were assessed and analyzed. The analysis of the distribution of sequences of coding DNA (genes and exons) and noncoding DNA (intergenic sequences and introns) revealed their universal pattern in genomes of all eukaryotes independently of their evolutionary level, the average number of introns in a gene, their sizes and the total genome size. It allows claiming that mechanisms of genomic reorganizations as a result of insertions, deletions, mutagenesis, duplications and others exhibit universal character. The size of inserted/deleted sites of DNA directly depends on the average size of the respective structural elements of a genetic code (genes, introns, exons) of the organism. Therefore the genetic engineering designs where the DNA donor and recipient are located at different evolutionary levels require the structural elements of foreign DNA being adapted to their average sizes of the host to minimize the negative effects from the reorganization of the genetic machinery of the host.
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34

DI GIULIO, MASSIMO. "The Non-universality of the Genetic Code: the Universal Ancestor was a Progenote." Journal of Theoretical Biology 209, no. 3 (2001): 345–49. http://dx.doi.org/10.1006/jtbi.2001.2271.

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35

Mustapha Abdulsalam, Fatima Zarah Yerima Ubah, Hasiya Ummi Ahmed, Ummulkhulthum Ahmed Tafida, and Aisha Wada Nasir. "Deciphering the Genetic Code: Mechanisms, Evolution, and Implications for Biotechnology." World Journal of Advanced Research and Reviews 21, no. 1 (2024): 858–68. http://dx.doi.org/10.30574/wjarr.2024.21.1.2195.

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The study of the genetic code explores the foundational language of life, aiming to fathom how DNA orchestrates the synthesis of proteins. This study explores various facets of the genetic code, from the widespread use of the triplet codon system to the vital role of transfer RNA (tRNA) in translation. This study unravels the intricacies of interactions between codons and anticodons, as well as the orchestration of ribosomes, casting illumination on the initiation, elongation, and termination stages of protein synthesis. Furthermore, it delves into the regulatory factors and mechanisms for quality control that wield influence over the translation processes. In the exploration of the genetic code's evolution, the study meticulously examines its universal principles, exceptions, and the compelling conjectures enveloping its origins. The coevolution of tRNA and codons, along with adaptations in the code observed in diverse organisms and organelles, yields valuable insights. Notably, the research underscores the vast biotechnological applications encompassing genetic engineering, codon optimization, and protein design. This study not only addresses uncharted territories in genetic code research but also propounds future research directions. It highlights current challenges and opportunities within this domain, including code expansion and gene editing advancement. Ultimately, the study of the genetic code remains a dynamic, ever-evolving field with profound implications for science, technology, and our comprehension of life's fundamental processes. This research unravels the captivating narrative of the genetic code, revealing novel areas and applications that continue to captivate and inspire.
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36

Mustapha, Abdulsalam, Zarah Yerima Ubah Fatima, Ummi Ahmed Hasiya, Ahmed Tafida Ummulkhulthum, and Wada Nasir Aisha. "Deciphering the Genetic Code: Mechanisms, Evolution, and Implications for Biotechnology." World Journal of Advanced Research and Reviews 21, no. 1 (2024): 858–68. https://doi.org/10.5281/zenodo.13221050.

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The study of the genetic code explores the foundational language of life, aiming to fathom how DNA orchestrates the synthesis of proteins. This study explores various facets of the genetic code, from the widespread use of the triplet codon system to the vital role of transfer RNA (tRNA) in translation. This study unravels the intricacies of interactions between codons and anticodons, as well as the orchestration of ribosomes, casting illumination on the initiation, elongation, and termination stages of protein synthesis. Furthermore, it delves into the regulatory factors and mechanisms for quality control that wield influence over the translation processes. In the exploration of the genetic code's evolution, the study meticulously examines its universal principles, exceptions, and the compelling conjectures enveloping its origins. The coevolution of tRNA and codons, along with adaptations in the code observed in diverse organisms and organelles, yields valuable insights. Notably, the research underscores the vast biotechnological applications encompassing genetic engineering, codon optimization, and protein design. This study not only addresses uncharted territories in genetic code research but also propounds future research directions. It highlights current challenges and opportunities within this domain, including code expansion and gene editing advancement. Ultimately, the study of the genetic code remains a dynamic, ever-evolving field with profound implications for science, technology, and our comprehension of life's fundamental processes. This research unravels the captivating narrative of the genetic code, revealing novel areas and applications that continue to captivate and inspire.
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37

Rosandić, Marija, and Vladimir Paar. "The Supersymmetry Genetic Code Table and Quadruplet Symmetries of DNA Molecules Are Unchangeable and Synchronized with Codon-Free Energy Mapping during Evolution." Genes 14, no. 12 (2023): 2200. http://dx.doi.org/10.3390/genes14122200.

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The Supersymmetry Genetic code (SSyGC) table is based on five physicochemical symmetries: (1) double mirror symmetry on the principle of the horizontal and vertical mirror symmetry axis between all bases (purines [A, G) and pyrimidines (U, C)] and (2) of bases in the form of codons; (3) direct–complement like codon/anticodon symmetry in the sixteen alternating boxes of the genetic code columns; (4) A + T-rich and C + G-rich alternate codons in the same row between both columns of the genetic code; (5) the same position between divided and undivided codon boxes in relation to horizontal mirror symmetry axes. The SSyGC table has a unique physicochemical purine–pyrimidine symmetry net which is as the core symmetry common for all, with more than thirty different nuclear and mitochondrial genetic codes. This net is present in the SSyGC table of all RNA and DNA living species. None of these symmetries are present in the Standard Genetic Code (SGC) table which is constructed on the alphabetic horizontal and vertical U-C-A-G order of bases. Here, we show that the free energy value of each codon incorporated as fundamentally mapping the “energy code” in the SSyGC table is compatible with mirror symmetry. On the other hand, in the SGC table, the same free energy values of codons are dispersed and a mirror symmetry between them is not recognizable. At the same time, the mirror symmetry of the SSyGC table and the DNA quadruplets together with our classification of codons/trinucleotides are perfectly imbedded in the mirror symmetry energy mapping of codons/trinucleotides and point out in favor of maintaining the integrity of the genetic code and DNA genome. We also argue that physicochemical symmetries of the SSyGC table in the manner of the purine–pyrimidine symmetry net, the quadruplet symmetry of DNA molecule, and the free energy of codons have remined unchanged during all of evolution. The unchangeable and universal symmetry properties of the genetic code, DNA molecules, and the energy code are decreasing disorder between codons/trinucleotides and shed a new light on evolution. Diversity in all living species on Earth is broad, but the symmetries of the Supersymmetry Genetic Code as the code of life and the DNA quadruplets related to the “energy code” are unique, unchangeable, and have the power of natural laws.
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38

Bakhtiyarov, K. I. "METALOGIC: THE REVIVAL OF LOGIC." Metaphysics, no. 1 (December 15, 2021): 176–82. http://dx.doi.org/10.22363/2224-7580-2021-1-176-182.

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As shown in the article, a single-level matrix of two-dimensional binarity represents 4 modes of time, 4 phases of genesis, 4 letters of the genetic code. The two-level matrix allows you to represent codons, 16 psychotypes, 16 tenses of the English verb, supergenesis. The three-level matrix gives triplets of the genetic code and a model of the conscious mind. For three universal paradigms of binarity, the logics of Boole, Lukasiewicz and metalogic were built, but the latter are still not used in computers. You need the CrossWord program instead of Word.
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39

Gospodinov, Anastas, and Dimiter Kunnev. "Universal Codons with Enrichment from GC to AU Nucleotide Composition Reveal a Chronological Assignment from Early to Late Along with LUCA Formation." Life 10, no. 6 (2020): 81. http://dx.doi.org/10.3390/life10060081.

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The emergence of a primitive genetic code should be considered the most essential event during the origin of life. Almost a complete set of codons (as we know them) should have been established relatively early during the evolution of the last universal common ancestor (LUCA) from which all known organisms descended. Many hypotheses have been proposed to explain the driving forces and chronology of the evolution of the genetic code; however, none is commonly accepted. In the current paper, we explore the features of the genetic code that, in our view, reflect the mechanism and the chronological order of the origin of the genetic code. Our hypothesis postulates that the primordial RNA was mostly GC-rich, and this bias was reflected in the order of amino acid codon assignment. If we arrange the codons and their corresponding amino acids from GC-rich to AU-rich, we find that: 1. The amino acids encoded by GC-rich codons (Ala, Gly, Arg, and Pro) are those that contribute the most to the interactions with RNA (if incorporated into short peptides). 2. This order correlates with the addition of novel functions necessary for the evolution from simple to longer folded peptides. 3. The overlay of aminoacyl-tRNA synthetases (aaRS) to the amino acid order produces a distinctive zonal distribution for class I and class II suggesting an interdependent origin. These correlations could be explained by the active role of the bridge peptide (BP), which we proposed earlier in the evolution of the genetic code.
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40

Muthugobal, Bagayalakshmi Karuna Nidhi, Ganapathy Ramesh, Subbiah Parthasarathy, Suvaiyarasan Suvaithenamudhan, and Karuppasamy Muthuvel Prasath. "Gray code representation of the universal genetic code: Generation of never born protein sequences using Toeplitz matrix approach." Biosystems 198 (December 2020): 104280. http://dx.doi.org/10.1016/j.biosystems.2020.104280.

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41

Mamatha, Dadala Mary, Haripriya Kotagaram, B. Hemavathi, and Swetha Kumari Koduru. "Molecular Identification of Indian Bovine Genetic Resources through Cox Gene-Based Barcode and QR Code." UTTAR PRADESH JOURNAL OF ZOOLOGY 46, no. 12 (2025): 405–21. https://doi.org/10.56557/upjoz/2025/v46i125078.

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Objective: The objective of this study was to map Indian Bovine species based on DNA Barcoding and Big data analytics. Methods: 5 Indian Bovine species blood samples were collected and performed molecular study. The whole DNA was isolated and the mitochondrial CoX gene was amplified in each species using Universal primers. The generated sequences were submitted to the BOLD Database to generate DNA Barcodes. The data was examined by the database and the respective DNA Barcodes were generated. Based on DNA Barcodes, using Python code, unique QR codes were generated. Further, based on the Morphological features, molecular features, DNA Barcodes, QR codes, and image data analysis were performed. Results: The isolated DNA was validated using Agarose Gel Electrophoresis. The PCR conditions for mitochondrial CoX gene amplification were standardized and purified followed by DNA Sequencing. 5DNABarcodes for Indian Bovine species were generated and uploaded to the BOLD database. QR codes were generated and Bid data analysis was performed using models for authenticated identification of Bovine species. Conclusion: In conclusion, the molecular mapping of Indian bovine genetic resources using DNA-based techniques such as bar coding, QR code technology, and big-data analysis provides a powerful framework for understanding and conserving the genetic diversity of bovine populations in India. The integration of DNA barcoding enables precise identification and classification of bovine breeds, while QR code technology offers an ovel and efficient means of tracking and monitoring genetic data in real time. The application of big-data analysis further strengthens the ability to detect patterns of genetic variation, assess breed composition, and identify areas of genetic erosion or introgression, which are crucial for breed conservation and improvement programs.
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42

Goldenfeld, Nigel, Tommaso Biancalani, and Farshid Jafarpour. "Universal biology and the statistical mechanics of early life." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 375, no. 2109 (2017): 20160341. http://dx.doi.org/10.1098/rsta.2016.0341.

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All known life on the Earth exhibits at least two non-trivial common features: the canonical genetic code and biological homochirality, both of which emerged prior to the Last Universal Common Ancestor state. This article describes recent efforts to provide a narrative of this epoch using tools from statistical mechanics. During the emergence of self-replicating life far from equilibrium in a period of chemical evolution, minimal models of autocatalysis show that homochirality would have necessarily co-evolved along with the efficiency of early-life self-replicators. Dynamical system models of the evolution of the genetic code must explain its universality and its highly refined error-minimization properties. These have both been accounted for in a scenario where life arose from a collective, networked phase where there was no notion of species and perhaps even individuality itself. We show how this phase ultimately terminated during an event sometimes known as the Darwinian transition, leading to the present epoch of tree-like vertical descent of organismal lineages. These examples illustrate concrete examples of universal biology: the quest for a fundamental understanding of the basic properties of living systems, independent of precise instantiation in chemistry or other media. This article is part of the themed issue ‘Reconceptualizing the origins of life’.
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43

Hendrickson, Tamara L., Whitney N. Wood, and Udumbara M. Rathnayake. "Did Amino Acid Side Chain Reactivity Dictate the Composition and Timing of Aminoacyl-tRNA Synthetase Evolution?" Genes 12, no. 3 (2021): 409. http://dx.doi.org/10.3390/genes12030409.

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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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44

Watanabe, Kimitsuna, and Shin-ichi Yokobori. "tRNA Modification and Genetic Code Variations in Animal Mitochondria." Journal of Nucleic Acids 2011 (2011): 1–12. http://dx.doi.org/10.4061/2011/623095.

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In animal mitochondria, six codons have been known as nonuniversal genetic codes, which vary in the course of animal evolution. They are UGA (termination codon in the universal genetic code changes to Trp codon in all animal mitochondria), AUA (Ile to Met in most metazoan mitochondria), AAA (Lys to Asn in echinoderm and some platyhelminth mitochondria), AGA/AGG (Arg to Ser in most invertebrate, Arg to Gly in tunicate, and Arg to termination in vertebrate mitochondria), and UAA (termination to Tyr in a planaria and a nematode mitochondria, but conclusive evidence is lacking in this case). We have elucidated that the anticodons of tRNAs deciphering these nonuniversal codons ( for UGA, for AUA, for AAA, and and for AGA/AGG) are all modified; has 5-carboxymethylaminomethyluridine or 5-taurinomethyluridine, has 5-formylcytidine or 5-taurinomethyluridine, has 7-methylguanosine and has 5-taurinomethyluridine in their anticodon wobble position, and has pseudouridine in the anticodon second position. This review aims to clarify the structural relationship between these nonuniversal codons and the corresponding tRNA anticodons including modified nucleosides and to speculate on the possible mechanisms for explaining the evolutional changes of these nonuniversal codons in the course of animal evolution.
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45

Nagao, Asuteka, Mitsuhiro Ohara, Kenjyo Miyauchi, et al. "Hydroxylation of a conserved tRNA modification establishes non-universal genetic code in echinoderm mitochondria." Nature Structural & Molecular Biology 24, no. 9 (2017): 778–82. http://dx.doi.org/10.1038/nsmb.3449.

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46

Vihinen, Mauno. "When a Synonymous Variant Is Nonsynonymous." Genes 13, no. 8 (2022): 1485. http://dx.doi.org/10.3390/genes13081485.

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Term synonymous variation is widely used, but frequently in a wrong or misleading meaning and context. Twenty three point eight % of possible nucleotide substitution types in the universal genetic code are for synonymous amino acid changes, but when these variants have a phenotype and functional effect, they are very seldom synonymous. Such variants may manifest changes at DNA, RNA and/or protein levels. Large numbers of variations are erroneously annotated as synonymous, which causes problems e.g., in clinical genetics and diagnosis of diseases. To facilitate precise communication, novel systematics and nomenclature are introduced for variants that when looking only at the genetic code seem like synonymous, but which have phenotypes. A new term, unsense variant is defined as a substitution in the mRNA coding region that affects gene expression and protein production without introducing a stop codon in the variation site. Such variants are common and need to be correctly annotated. Proper naming and annotation are important also to increase awareness of these variants and their consequences.
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47

Chatterjee, Sankar, and Surya Yadav. "The Origin of Prebiotic Information System in the Peptide/RNA World: A Simulation Model of the Evolution of Translation and the Genetic Code." Life 9, no. 1 (2019): 25. http://dx.doi.org/10.3390/life9010025.

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Information is the currency of life, but the origin of prebiotic information remains a mystery. We propose transitional pathways from the cosmic building blocks of life to the complex prebiotic organic chemistry that led to the origin of information systems. The prebiotic information system, specifically the genetic code, is segregated, linear, and digital, and it appeared before the emergence of DNA. In the peptide/RNA world, lipid membranes randomly encapsulated amino acids, RNA, and peptide molecules, which are drawn from the prebiotic soup, to initiate a molecular symbiosis inside the protocells. This endosymbiosis led to the hierarchical emergence of several requisite components of the translation machine: transfer RNAs (tRNAs), aminoacyl-tRNA synthetase (aaRS), messenger RNAs (mRNAs), ribosomes, and various enzymes. When assembled in the right order, the translation machine created proteins, a process that transferred information from mRNAs to assemble amino acids into polypeptide chains. This was the beginning of the prebiotic <i>information</i> age. The origin of the genetic code is enigmatic; herein, we propose an evolutionary explanation: the demand for a wide range of protein enzymes over peptides in the prebiotic reactions was the main selective pressure for the origin of information-directed protein synthesis. The molecular basis of the genetic code manifests itself in the interaction of aaRS and their cognate tRNAs. In the beginning, aminoacylated ribozymes used amino acids as a cofactor with the help of bridge peptides as a process for selection between amino acids and their cognate codons/anticodons. This process selects amino acids and RNA species for the next steps. The ribozymes would give rise to pre-tRNA and the bridge peptides to pre-aaRS. Later, variants would appear and evolution would produce different but specific aaRS-tRNA-amino acid combinations. Pre-tRNA designed and built pre-mRNA for the storage of information regarding its cognate amino acid. Each pre-mRNA strand became the storage device for the genetic information that encoded the amino acid sequences in triplet nucleotides. As information appeared in the digital languages of the codon within pre-mRNA and mRNA, and the genetic code for protein synthesis evolved, the prebiotic chemistry then became more organized and directional with the emergence of the translation and genetic code. The genetic code developed in three stages that are coincident with the refinement of the translation machines: the GNC code that was developed by the pre-tRNA/pre-aaRS /pre-mRNA machine, SNS code by the tRNA/aaRS/mRNA machine, and finally the universal genetic code by the tRNA/aaRS/mRNA/ribosome machine. We suggest the coevolution of translation machines and the genetic code. The emergence of the translation machines was the beginning of the Darwinian evolution, an interplay between information and its supporting structure. Our hypothesis provides the logical and incremental steps for the origin of the programmed protein synthesis. In order to better understand the prebiotic information system, we converted letter codons into numerical codons in the Universal Genetic Code Table. We have developed a software, called CATI (Codon-Amino Acid-Translator-Imitator), to translate randomly chosen numerical codons into corresponding amino acids and vice versa. This conversion has granted us insight into how the genetic code might have evolved in the peptide/RNA world. There is great potential in the application of numerical codons to bioinformatics, such as barcoding, DNA mining, or DNA fingerprinting. We constructed the likely biochemical pathways for the origin of translation and the genetic code using the Model-View-Controller (MVC) software framework, and the translation machinery step-by-step. While using AnyLogic software, we were able to simulate and visualize the entire evolution of the translation machines, amino acids, and the genetic code.
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48

Takagi, Hiroaki, Kunihiko Kaneko, and Tetsuya Yomo. "Evolution of Genetic Codes through Isologous Diversification of Cellular States." Artificial Life 6, no. 4 (2000): 283–305. http://dx.doi.org/10.1162/106454600300103647.

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Evolution of genetic codes is studied as change in the choice of enzymes that are used to synthesize amino acids from the genetic information of nucleic acids. We propose the following theory: the differentiation of physiological states of a cell allows for a choice of enzymes, and this choice is later fixed genetically through evolution. To demonstrate this theory, a dynamical systems model consisting of the concentrations of metabolites, enzymes, amino acyl tRNA synthetase, and tRNA–amino acid complexes in a cell is introduced and studied numerically. It is shown that the biochemical states of cells are differentiated by cell-cell interactions, and each differentiated type starts to use a different synthetase. Through the mutation of genes, this difference in the genetic code is amplified and stabilized. The relevance of this theory to the evolution of non-universal genetic code in mitochondria is suggested. The present theory is based on our recent theory of isologous symbiotic speciation, which is briefly reviewed. According to the theory, phenotypes of organisms are first differentiated into distinct types through the interaction and developmental dynamics, even though they have identical genotypes; later, with mutation in the genotype, the genotype also differentiates into discrete types, while maintaining the “symbiotic” relationship between the types. Relevance of the theory to natural as well as artificial evolution is discussed.
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49

Woese, Carl R., Gary J. Olsen, Michael Ibba, and Dieter Söll. "Aminoacyl-tRNA Synthetases, the Genetic Code, and the Evolutionary Process." Microbiology and Molecular Biology Reviews 64, no. 1 (2000): 202–36. http://dx.doi.org/10.1128/mmbr.64.1.202-236.2000.

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SUMMARY The aminoacyl-tRNA synthetases (AARSs) and their relationship to the genetic code are examined from the evolutionary perspective. Despite a loose correlation between codon assignments and AARS evolutionary relationships, the code is far too highly structured to have been ordered merely through the evolutionary wanderings of these enzymes. Nevertheless, the AARSs are very informative about the evolutionary process. Examination of the phylogenetic trees for each of the AARSs reveals the following. (i) Their evolutionary relationships mostly conform to established organismal phylogeny: a strong distinction exists between bacterial- and archaeal-type AARSs. (ii) Although the evolutionary profiles of the individual AARSs might be expected to be similar in general respects, they are not. It is argued that these differences in profiles reflect the stages in the evolutionary process when the taxonomic distributions of the individual AARSs became fixed, not the nature of the individual enzymes. (iii) Horizontal transfer of AARS genes between Bacteria and Archaea is asymmetric: transfer of archaeal AARSs to the Bacteria is more prevalent than the reverse, which is seen only for the “gemini group.” (iv) The most far-ranging transfers of AARS genes have tended to occur in the distant evolutionary past, before or during formation of the primary organismal domains. These findings are also used to refine the theory that at the evolutionary stage represented by the root of the universal phylogenetic tree, cells were far more primitive than their modern counterparts and thus exchanged genetic material in far less restricted ways, in effect evolving in a communal sense.
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50

Shcherbak, Vladimir I. "A new manifestation of the arithmetical regularity suggests the universal genetic code distinguishes the decimal system." Origins of Life and Evolution of the Biosphere 26, no. 3-5 (1996): 442–43. http://dx.doi.org/10.1007/bf02459858.

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