Anticodon Modifications in the tRNA Set of LUCA and the Fundamental Regularity in the Standard Genetic Code

Gulik, Peter T. S. van der; Hoff, Wouter D.

doi:10.1371/journal.pone.0158342

Cited by 18 publications

(18 citation statements)

References 73 publications

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“…The distribution of single- and multiple-meaning boxes follows the complete symmetry without any deviation (Figure 10b). These characters did not catch the attention of previous observers beyond the level of decoding where the explanation involves formation of codon: anticodon pairs [19,72,91]. The participation of anticodon dimers did not need to be invoked since questionings were satisfied by the decoding function only.…”

Section: Symmetries and Error-reduction In Modularitymentioning

confidence: 90%

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

Guimarães

2017

Life

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The proposal that the genetic code was formed on the basis of (proto)tRNA Dimer-Directed Protein Synthesis is reviewed and updated. The tRNAs paired through the anticodon loops are an indication on the process. Dimers are considered mimics of the ribosomes—structures that hold tRNAs together and facilitate the transferase reaction, and of the translation process—anticodons are at the same time codons for each other. The primitive protein synthesis system gets stabilized when the product peptides are stable and apt to bind the producers therewith establishing a self-stimulating production cycle. The chronology of amino acid encoding starts with Glycine and Serine, indicating the metabolic support of the Glycine-Serine C1-assimilation pathway, which is also consistent with evidence on origins of bioenergetics mechanisms. Since it is not possible to reach for substrates simpler than C1 and compounds in the identified pathway are apt for generating the other central metabolic routes, it is considered that protein synthesis is the beginning and center of a succession of sink-effective mechanisms that drive the formation and evolution of the metabolic flow system. Plasticity and diversification of proteins construct the cellular system following the orientation given by the flow and implementing it. Nucleic acid monomers participate in bioenergetics and the polymers are conservative memory systems for the synthesis of proteins. Protoplasmic fission is the final sink-effective mechanism, part of cell reproduction, guaranteeing that proteins don’t accumulate to saturation, which would trigger inhibition.

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Section: Symmetries and Error-reduction In Modularitymentioning

confidence: 90%

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

Guimarães

2017

Life

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“…One is that the Last Universal Common Ancestor (LUCA) had evolved a full set of 61 genetic codons, but the tRNA-ANNs are lost in the common ancestor of Archaea. Another hypothesis is that the LUCA had only the minimum set of tRNAs (44 or 45 different types) to decode all codons before the appearance of the three life domains ( van der Gulik and Hoff, 2016 ). The types of tRNA for most archaeal genomes across different phylogenetic clades are coincident with this number.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Analysis Reveals Ancestral Lack of Seventeen Different tRNAs and Clade-Specific Loss of tRNA-CNNs in Archaea

Wang

Shao

2018

Front. Microbiol.

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Transfer RNA (tRNA) is a category of RNAs that specifically decode messenger RNAs (mRNAs) into proteins by recognizing a set of 61 codons commonly adopted by different life domains. The composition and abundance of tRNAs play critical roles in shaping codon usage and pairing bias, which subsequently modulate mRNA translation efficiency and accuracy. Over the past few decades, effort has been concentrated on evaluating the specificity and redundancy of different tRNA families. However, the mechanism and processes underlying tRNA evolution have only rarely been investigated. In this study, by surveying tRNA genes in 167 completely sequenced genomes, we systematically investigated the composition and evolution of tRNAs in Archaea from a phylogenetic perspective. Our data revealed that archaeal genomes are compact in both tRNA types and copy number. Generally, no more than 44 different types of tRNA are present in archaeal genomes to decode the 61 canonical codons, and most of them have only one gene copy per genome. Among them, tRNA-Met was significantly overrepresented, with an average of three copies per genome. In contrast, the tRNA-UAU and 16 tRNAs with A-starting anticodons (tRNA-ANNs) were rarely detected in all archaeal genomes. The conspicuous absence of these tRNAs across the archaeal phylogeny suggests they might have not been evolved in the common ancestor of Archaea, rather than have lost independently from different clades. Furthermore, widespread absence of tRNA-CNNs in the Methanococcales and Methanobacteriales genomes indicates convergent loss of these tRNAs in the two clades. This clade-specific tRNA loss may be attributing to the reductive evolution of their genomes. Our data suggest that the current tRNA profiles in Archaea are contributed not only by the ancestral tRNA composition, but also by differential maintenance and loss of redundant tRNAs.

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“…In the same line of thoughts, doublet codings may have been associated to reverse recognition in earlier times of life organisms [18,19]. This prompted the authors of Ref.…”

Section: 2mentioning

confidence: 99%

Complete Quantum Information in the DNA Genetic Code

Planat¹,

Aschheim²,

Amaral³

et al. 2020

Preprint

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We find that the degeneracies and many peculiarities of the DNA genetic code may be described thanks to two closely related (fivefold symmetric) finite groups. The first group has signature $G=\mathbb{Z}_5 \rtimes H$ where $H=\mathbb{Z}_2 . S_4\cong 2O$ is isomorphic to the binary octahedral group $2O$ and $S_4$ is the symmetric group on four letters/bases. The second group has signature $G=\mathbb{Z}_5 \rtimes GL(2,3)$ and points out a threefold symmetry of base pairings. For those groups, the representations for the $22$ conjugacy classes of $G$ are in one-to-one correspondence with the multiplets encoding the proteinogenic amino acids. Additionally, most of the $22$ characters of $G$ attached to those representations are informationally complete. The biological meaning of these coincidences is discussed.

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Anticodon Modifications in the tRNA Set of LUCA and the Fundamental Regularity in the Standard Genetic Code

Cited by 18 publications

References 73 publications

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

Self-Referential Encoding on Modules of Anticodon Pairs—Roots of the Biological Flow System

Genome-Wide Analysis Reveals Ancestral Lack of Seventeen Different tRNAs and Clade-Specific Loss of tRNA-CNNs in Archaea

Complete Quantum Information in the DNA Genetic Code

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