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Life
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The Origins and Evolution of the Genetic Code
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The Origins and Evolution of the Genetic Code

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Origin of Life".

Deadline for manuscript submissions: closed (30 April 2024) | Viewed by 2337

Special Issue Editor

Prof. Kenji Ikehara

E-Mail Website
Guest Editor
1. G&L Kyosei Institute in The Keihanna Academy of Science and Culture (KASC), Keihanna Interaction Plaza, Lab. Wing 3F, 1-7 Hikaridai, Seika-cho, Souraku, Kyoto 619-0237, Japan
2. The International Institute for Advanced Studies, Kizugawadai 9-3, Kizugawa, Kyoto 619-0225, Japan
Interests: the origin of life; the origin and evolution of the genetic code; the origin and evolution of genes; the origin and evolution of proteins
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The genetic code connecting genes with proteins is one key member of the core life system and is composed of three members (gene, tRNA, genetic code and protein). Therefore, the origin of the genetic code, which is deeply involved in the origin of life, has been studied by many researchers thus far. However, the idea explaining from what code the genetic code originated and how the first code evolved into the universal (standard) genetic code has not yet been established. The main reasons before this are as follows.

  1. Studies on the origin of the genetic code are carried out mainly based on stereochemical theory, based on which it is quite difficult to establish direct corresponding relationships between amino acids and codons or anticodons.
  2. The origins of tRNA and aminoacyl-tRNA synthetase (aaRS), both of which are intimately related to the formation of the genetic code, still remain unclear.

On the other hand, elucidation of the evolution of the genetic code is of course quite important, because the evolutionary pathway should progress in parallel with the evolutionary processes of genes and proteins. However, the evolutionary pathway of the genetic code also remains unsolved, irrespective of strenuous efforts of many researchers. Therefore, it is necessary to make clear the following things:

  1. What amino acids were used in the most primeval genetic code and what types of amino acids were captured in the most primeval genetic code and in what order to complete the modern genetic code?
  2. It Whether or not there was a division of roles between the first amino acids and amino acids introduced later into the first genetic code.

The purpose of this Special Issue is to discuss the origin and evolution of the genetic code. Therefore, I am looking forward to receiving many papers discussing the origins and evolution of tRNA, aminoacyl-tRNA synthetase (aaRS), amino acid metabolism, genes and proteins, in addition to the origin and evolution of the genetic code.

Prof. Kenji Ikehara
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • origin of the genetic code
  • origin of tRNA
  • origin of amino acid metabolism
  • origin of genes
  • origin of proteins
  • origin of life
  • evolution of the genetic code
  • evolution of amino acid metabolism
  • evolution of genes
  • evolution of proteins

Published Papers (2 papers)

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Research

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24 pages, 3099 KiB  
Article
Groups of Symmetries of the Two Classes of Synthetases in the Four-Dimensional Hypercubes of the Extended Code Type II
by Marco V. José, Eberto R. Morgado and Juan R. Bobadilla
Life 2023, 13(10), 2002; https://doi.org/10.3390/life13102002 - 30 Sep 2023
Viewed by 778
Abstract
Aminoacyl-tRNA synthetases (aaRSs) originated from an ancestral bidirectional gene (mirror symmetry), and through the evolution of the genetic code, the twenty aaRSs exhibit a symmetrical distribution in a 6-dimensional hypercube of the Standard Genetic Code. In this work, we assume a primeval RNY [...] Read more.
Aminoacyl-tRNA synthetases (aaRSs) originated from an ancestral bidirectional gene (mirror symmetry), and through the evolution of the genetic code, the twenty aaRSs exhibit a symmetrical distribution in a 6-dimensional hypercube of the Standard Genetic Code. In this work, we assume a primeval RNY code and the Extended Genetic RNA code type II, which includes codons of the types YNY, YNR, and RNR. Each of the four subsets of codons can be represented in a 4-dimensional hypercube. Altogether, these 4 subcodes constitute the 6-dimensional representation of the SGC. We identify the aaRSs symmetry groups in each of these hypercubes. We show that each of the four hypercubes contains the following sets of symmetries for the two known Classes of synthetases: RNY: dihedral group of order 4; YNY: binary group; YNR: amplified octahedral group; and RNR: binary group. We demonstrate that for each hypercube, the group of symmetries in Class 1 is the same as the group of symmetries in Class 2. The biological implications of these findings are discussed. Full article
(This article belongs to the Special Issue The Origins and Evolution of the Genetic Code)
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Review

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19 pages, 3256 KiB  
Review
Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction
by Charles W. Carter, Jr.
Life 2024, 14(2), 199; https://doi.org/10.3390/life14020199 - 30 Jan 2024
Viewed by 1069
Abstract
How Nature discovered genetic coding is a largely ignored question, yet the answer is key to explaining the transition from biochemical building blocks to life. Other, related puzzles also fall inside the aegis enclosing the codes themselves. The peptide bond is unstable with [...] Read more.
How Nature discovered genetic coding is a largely ignored question, yet the answer is key to explaining the transition from biochemical building blocks to life. Other, related puzzles also fall inside the aegis enclosing the codes themselves. The peptide bond is unstable with respect to hydrolysis. So, it requires some form of chemical free energy to drive it. Amino acid activation and acyl transfer are also slow and must be catalyzed. All living things must thus also convert free energy and synchronize cellular chemistry. Most importantly, functional proteins occupy only small, isolated regions of sequence space. Nature evolved heritable symbolic data processing to seek out and use those sequences. That system has three parts: a memory of how amino acids behave in solution and inside proteins, a set of code keys to access that memory, and a scoring function. The code keys themselves are the genes for cognate pairs of tRNA and aminoacyl-tRNA synthetases, AARSs. The scoring function is the enzymatic specificity constant, kcat/kM, which measures both catalysis and specificity. The work described here deepens the evidence for and understanding of an unexpected consequence of ancestral bidirectional coding. Secondary structures occur in approximately the same places within antiparallel alignments of their gene products. However, the polar amino acids that define the molecular surface of one are reflected into core-defining non-polar side chains on the other. Proteins translated from base-paired coding strands fold up inside out. Bidirectional genes thus project an inverted structural duality into the proteome. I review how experimental data root the scoring functions responsible for the origins of coding and catalyzed activation of unfavorable chemical reactions in that duality. Full article
(This article belongs to the Special Issue The Origins and Evolution of the Genetic Code)
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