Origins of gene, genetic code, protein and life: comprehensive view of life systems from a GNC-SNS primitive genetic code hypothesis

“…five amino acids like those found in the Miller–Urey experiments and the Murchison meteorite (Miller et al. 1976), and that the genetic code was initially limited to these few amino acids that still predominate in proteins to the current day (e.g. Trifonov 2000; Brooks et al. 2002; Ikehara 2002).”

“SNS is composed of 10 amino acids (glycine, alanine, aspartic acid, valine, glutamic acid, leucine, proline, histidine, glutamine, and arginine) and 16 codons (GGC, GGG, GCC, GCG, GAC, GAG, GUC, GUG, CUC, GUG, CCC, CGC, CAC, CAG, CGC, and CGG) [87,88].”

“this is a viewpoint held by some leading scientists working in the field [13,19,20].”

“A possible evolutionary process of emergence of life based upon the GADV hypothesis is as follows [5,6,23].”

“…in the [GADV]-protein world could accumulate [GADV]-proteins through their pseudo-replication in the absence of genes as we have proposed (Ikehara, 2001, 2002), the [GADV]-proteins in the protein world were not even the simplest life itself, since the proteins could not evolve in the…”

“The theory of Ikehara [reviewed in [96,97]] about the origins of gene, genetic code, protein and life is especially interesting regarding the Proteomic Code.”

“To this end, I have proposed the [GADV]-protein world hypothesis, or the GADV hypothesis in short, for the origin of life (Ikehara 2002; Ikehara 2005; Ikehara 2009; Ikehara 2012).”

“…the RRY code (R=G or A, Y=C or T) with eight trinucleotides and four amino acids (Crick et al. 1976), the RNY code (N=any nucleotide) with 16 trinucleotides and eight amino acids (Eigen and Schuster 1978; Shepherd 1981), or the GNC code with four trinucleotides and four amino acids (Ikehara 2002).”

“They share this characteristic with the scenarios published by Wong [54] and by Ikehara [55].”

“It is also worth mentioning that the genetic code presumably evolved to alternate in response to changing environments by assigning the thermostable nucleotides GC to codons that encode thermostabilizing amino acid residues (Xia and Li 1998; Ikehara 2002).”

“Many examples of such ancient genetic codes have been proposed, including the codes RRY of size 8 [18] and RNY of size 16 [19,20] (R = {A, G}, Y = {C, T}, N = {A, C, G, T}), the codes GNC of size 4 and SNS of size 16 [21], and GHN of size 12 [22] (S = {C, G}, H = {A, C, T}), etc.”

“In addition, we have also showed that probabilities of two neighboring amino acids calculated from a multiplication of two average amino acid compositions are close to the average appearance frequencies that are actually detected in proteins encoded by microbial genomes (Ikehara 2002).”

“In the next stage of coded peptide synthesis, Asp and Val could have been added to the repertoire (see e.g. Ardell 1998; Eigen and Schuster 1978; van der Gulik et al. 2009; Higgs 2009; Ikehara 2002).”

“The GADV protein world hypothesis is based on the observation that proteins containing approximately equal amounts of four amino acids – glycine (G, Gly), ala nine (A, Ala), aspartic acid (D, Asp), and valine (V, Val) – could form major secondary protein structures, such as α helices and β sheets [117, 118].”

“…deleted from the cyclic pathway and the connection between Ala (GGC) and Ala (TGC) was remained, because the latter tRNAs for translating one of [GADV]-amino acids should be more fundamental than the former, judging from GNC-SNS primitive genetic code hypothesis (Ikehara 2002; Ikehara et al. 2002).”

“Furthermore, Francis (2013) considers the hypothesis that very early on the genetic code used only codons of the GNC kind (Ikehara 2002; Trifonov 2004; Francis 2011), a code completely compatible also with the coevolution theory (Di Giulio 2008a).”

“He hypothesized that proteins were originally produced by the random peptide formation of amino acids restricted to specific amino acid compositions and that newly born genes were products of nonstop frames on antisense strands of microbial GC-rich or GCG repeating sequences.[11] Ogata and Miura reported that the gene…”

“Further, it is also confirmed that [GADV]-amino acid composition is the simplest combination among twenty amino acids, which satisfies the four conditions for water-soluble globular protein formation [15].”

“proposed in their hypothesis a [glycine, alanine, aspartic acid, and valine (GADV)]-protein world hypothesis on the origin of life, based on the GNC code encoding amino acids as the most primitive genetic code [21].”

“2014)—possibly as few as four (Ikehara 2002)—need to have been provided in this way.”

“Since the discovery of the genetic code, many attempts have been made to find its simpler predecessors (see for instance, Crick 1968, Kolaskar and Ramabrahmam 1982, Ikehara 2002).”

“Furthermore, Ikehara concluded from the analysis of microbial genes that newly-born genes are products of nonstop frames (NSF) on antisense strands of microbial GC-rich genes [GCNSF(antisense)] and from SNS repeating sequences [(SNS)n] similar to the GC-NSF(antisense).”

“(Ikehara 2002, 165; also see Gusev, Schulze-Makuch 2004).”

“The reason the four types of [GADV]-amino acids were chosen as components of the most primitive protein is not only because the [GADV]-amino acids were able to be easily produced via prebiotic means and accumulated in large amounts on primitive Earth, but also because [GADV]-amino acids satisfy the four conditions (hy…”

“Ikehara [69] hinted that the universal genetic code with 64 codons originated from the SNS code which allowed redundancy.”

“[17] Ikehara K (2002) Origins of gene, genetic code, protein and life: comprehensive view of life system from a GNC-SNS primitive genetic code hypothesis.”

“…a novel hypothesis on the origin of life as GADV hypothesis, suggesting that life originated from [GADV]-protein world, which was composed of [GADV]-proteins accumulated by pseudoreplication of the proteins in the absence of any genetic function (Ikehara, 2002; Ikehara, 2005, Ikehara, 2009).”