Fossil remnants of a primeval genetic code in all forms of life?

Why Were [GADV]-amino Acids and GNC Codons Selected and How Was GNC Primeval Genetic Code Established?

Correspondence relations between codons and amino acids are determined by genetic code. Therefore, genetic code holds a key of the life system composed of genes and protein. According to the GNC-SNS primitive genetic code hypothesis, which I have proposed, it is assumed that the genetic code originated from GNC code. In this article, first, it is discussed from a standpoint of primeval protein synthesis, why four [GADV]-amino acids were selected and used in the first GNC code. Next, it is explained from another standpoint of the most primitive anticodon-stem loop tRNAs (AntiC-SL tRNAs), how four GNCs were selected for the first codons. Furthermore, in the last section of this article, I will explain my idea of how the correspondence relations between four [GADV]-amino acids and four GNC codons were established. Namely, the origin and evolution of the genetic code was discussed comprehensively from several aspects of [GADV]-proteins, [GADV]-amino acids, GNC codons, and anticodon stem-loop tRNAs (AntiC-SL tRNAs), which relate each other to the origin of the genetic code, as integrating GNC code frozen-accident theory, coevolution theory, and adaptive theory on the origin of the genetic code.

On the Evolutionary History of the Twenty Encoded Amino Acids

α-Amino acids are essential molecular constituents of life, twenty of which are privileged because they are encoded by the ribosomal machinery. The question remains open as to why this number and why this 20 in particular, an almost philosophical question that cannot be conclusively resolved. They are closely related to the evolution of the genetic code and whether nucleic acids, amino acids, and peptides appeared simultaneously and were available under prebiotic conditions when the first self-sufficient complex molecular system emerged on Earth. This report focuses on prebiotic and metabolic aspects of amino acids and proteins starting with meteorites, followed by their formation, including peptides, under plausible prebiotic conditions, and the major biosynthetic pathways in the various kingdoms of life. Coenzymes play a key role in the present analysis in that amino acid metabolism is linked to glycolysis and different variants of the tricarboxylic acid cycle (TCA, rTCA, and the incomplete horseshoe version) as well as the biosynthesis of the most important coenzymes. Thus, the report opens additional perspectives and facets on the molecular evolution of primary metabolism.

Coevolution Theory of the Genetic Code at Age Forty: Pathway to Translation and Synthetic Life

The origins of the components of genetic coding are examined in the present study. Genetic information arose from replicator induction by metabolite in accordance with the metabolic expansion law. Messenger RNA and transfer RNA stemmed from a template for binding the aminoacyl-RNA synthetase ribozymes employed to synthesize peptide prosthetic groups on RNAs in the Peptidated RNA World. Coevolution of the genetic code with amino acid biosynthesis generated tRNA paralogs that identify a last universal common ancestor (LUCA) of extant life close to Methanopyrus, which in turn points to archaeal tRNA introns as the most primitive introns and the anticodon usage of Methanopyrus as an ancient mode of wobble. The prediction of the coevolution theory of the genetic code that the code should be a mutable code has led to the isolation of optional and mandatory synthetic life forms with altered protein alphabets.

On the prevalence of certain codons ("RNY") in genes for proteins

J.C. Shepherd notes that codons of the type RNY (R = purine, N = any nucleotide base, Y = pyrimidine) predominate over RNR in the genes for proteins. He has hypothesized that RNY codons are the relics of "a primitive code" composed of repeating RNY triplets. He found that RNY codons predominated in fourfold RNN codon sets (family boxes). These family boxes code for valine, threonine, alanine, and glycine. We argue that the proposed "comma-less" code composed of RNY never existed, and that, in any case, survival of such a code would have long since been erased by mutations. The excess of RNY codons in family boxes is probably attributable to preference for the corresponding tRNAs.

Natural selection versus primitive gene structure as determinant of codon usage

Different codons are not utilized equally in known gene sequences. One of the important biases of codon usage is observed in the form of an enrichment of RNY codons, especially within RNN codon families. Such biases could represent the residue of a primitive repeating-RNY gene structure, or the outcome of natural selection, or both. Analyses based on the rates of silent substitutions, the frequencies of base doublets, and synonymous codon ratios for Escherichia coli, yeast, Drosophila and Xenopus proteins have been performed. The results rule out any significant support for a primitive repeating-RNY or repeating-RRY gene structure, and establish the important role of natural selection in determining the choice of codons. With strong intervention by natural selection, the relationship between primitive gene structure and codon usage necessarily becomes minimal.