Evolution of the Standard Genetic Code

Ordering events in a developing genetic code

Preexisting partial genetic codes can fuse to evolve towards the complete Standard Genetic Code (SGC). Such code fusion provides a path of 'least selection', readily generating precursor codes that resemble the SGC. Consequently, such least selections produce the SGC via minimal, thus rapid, change. Optimal code evolution therefore requires delayed wobble. Early wobble encoding slows code evolution, very specifically diminishing the most likely SGC precursors: near-complete, accurate codes which are the products of code fusions. In contrast: given delayed wobble, the SGC can emerge from a truncation selection/evolutionary radiation based on proficient fused coding.

The 3 31 Nucleotide Minihelix tRNA Evolution Theorem and the Origin of Life

There are no theorems (proven theories) in the biological sciences. We propose that the 3 31 nt minihelix tRNA evolution theorem be universally accepted as one. The 3 31 nt minihelix theorem completely describes the evolution of type I and type II tRNAs from ordered precursors (RNA repeats and inverted repeats). Despite the diversification of tRNAome sequences, statistical tests overwhelmingly support the theorem. Furthermore, the theorem relates the dominant pathway for the origin of life on Earth, specifically, how tRNAomes and the genetic code may have coevolved. Alternate models for tRNA evolution (i.e., 2 minihelix, convergent and accretion models) are falsified. In the context of the pre-life world, tRNA was a molecule that, via mutation, could modify anticodon sequences and teach itself to code. Based on the tRNA sequence, we relate the clearest history to date of the chemical evolution of life. From analysis of tRNA evolution, ribozyme-mediated RNA ligation was a primary driving force in the evolution of complexity during the pre-life-to-life transition. TRNA formed the core for the evolution of living systems on Earth.

The Genetic Code Assembles via Division and Fusion, Basic Cellular Events

Standard Genetic Code (SGC) evolution is quantitatively modeled in up to 2000 independent coding 'environments'. Environments host multiple codes that may fuse or divide, with division yielding identical descendants. Code division may be selected-sophisticated gene products could be required for an orderly separation that preserves the coding. Several unforeseen results emerge: more rapid evolution requires unselective code division rather than its selective form. Combining selective and unselective code division, with/without code fusion, with/without independent environmental coding tables, and with/without wobble defines 25 = 32 possible pathways for SGC evolution. These 32 possible histories are compared, specifically, for evolutionary speed and code accuracy. Pathways differ greatly, for example, by ≈300-fold in time to evolve SGC-like codes. Eight of thirty-two pathways employing code division evolve quickly. Four of these eight that combine fusion and division also unite speed and accuracy. The two most precise, swiftest paths; thus the most likely routes to the SGC are similar, differing only in fusion with independent environmental codes. Code division instead of fusion with unrelated codes implies that exterior codes can be dispensable. Instead, a single ancestral code that divides and fuses can initiate fully encoded peptide biosynthesis. Division and fusion create a 'crescendo of competent coding', facilitating the search for the SGC and also assisting the advent of otherwise uniformly disfavored wobble coding. Code fusion can unite multiple codon assignment mechanisms. However, via code division and fusion, an SGC can emerge from a single primary origin via familiar cellular events.

The Evolution of Life Is a Road Paved with the DNA Quadruplet Symmetry and the Supersymmetry Genetic Code

Symmetries have not been completely determined and explained from the discovery of the DNA structure in 1953 and the genetic code in 1961. We show, during 10 years of investigation and research, our discovery of the Supersymmetry Genetic Code table in the form of 2 × 8 codon boxes, quadruplet DNA symmetries, and the classification of trinucleotides/codons, all built with the same physiochemical double mirror symmetry and Watson-Crick pairing. We also show that single-stranded RNA had the complete code of life in the form of the Supersymmetry Genetic Code table simultaneously with instructions of codons' relationship as to how to develop the DNA molecule on the principle of Watson-Crick pairing. We show that the same symmetries between the genetic code and DNA quadruplet are highly conserved during the whole evolution even between phylogenetically distant organisms. In this way, decreasing disorder and entropy enabled the evolution of living beings up to sophisticated species with cognitive features. Our hypothesis that all twenty amino acids are necessary for the origin of life on the Earth, which entirely changes our view on evolution, confirms the evidence of organic natural amino acids from the extra-terrestrial asteroid Ryugu, which is nearly as old as our solar system.

Mitochondrial genomes in the iconic reindeer lichens: Architecture, variation, and synteny across multiple evolutionary scales

Variation in mitochondrial genome composition across intraspecific, interspecific, and higher taxonomic scales has been little studied in lichen obligate symbioses. Cladonia is one of the most diverse and ecologically important lichen genera, with over 500 species representing an array of unique morphologies and chemical profiles. Here, we assess mitochondrial genome diversity and variation in this flagship genus, with focused sampling of two clades of the "true" reindeer lichens, Cladonia subgenus Cladina, and additional genomes from nine outgroup taxa. We describe composition and architecture at the gene and the genome scale, examining patterns in organellar genome size in larger taxonomic groups in Ascomycota. Mitochondrial genomes of Cladonia, Pilophorus, and Stereocaulon were consistently larger than those of Lepraria and contained more introns, suggesting a selective pressure in asexual morphology in Lepraria driving it toward genomic simplification. Collectively, lichen mitochondrial genomes were larger than most other fungal life strategies, reaffirming the notion that coevolutionary streamlining does not correlate to genome size reductions. Genomes from Cladonia ravenelii and Stereocaulon pileatum exhibited ATP9 duplication, bearing paralogs that may still be functional. Homing endonuclease genes (HEGs), though scarce in Lepraria, were diverse and abundant in Cladonia, exhibiting variable evolutionary histories that were sometimes independent of the mitochondrial evolutionary history. Intraspecific HEG diversity was also high, with C. rangiferina especially bearing a range of HEGs with one unique to the species. This study reveals a rich history of events that have transformed mitochondrial genomes of Cladonia and related genera, allowing future study alongside a wealth of assembled genomes.

A crescendo of competent coding (c3) contains the Standard Genetic Code

The Standard Genetic Code (SGC) can arise by fusion of partial codes evolved in different individuals, perhaps for differing prior tasks. Such code fragments can be unified into an SGC after later evolution of accurate third-position Crick wobble. Late wobble advent fills in the coding table, leaving only later development of translational initiation and termination to reach the SGC in separated domains of life. This code fusion mechanism is computationally implemented here. Late Crick wobble after C3 fusion (c3-lCw) is tested for its ability to evolve the SGC. Compared with previously studied isolated coding tables, or with increasing numbers of parallel, but nonfusing codes, c3-lCw reaches the SGC sooner, is successful in a smaller population, and presents accurate and complete codes more frequently. Notably, a long crescendo of SGC-like codes is exposed for selection of superior translation. c3-lCw also effectively suppresses varied disordered assignments, thus converging on a unified code. Such merged codes closely approach the SGC, making its selection plausible. For example: Under routine conditions, ≈1 of 22 c3-lCw environments evolves codes with ≥20 assignments and ≤3 differences from the SGC, notably including codes identical to the Standard Genetic Code.

“Superwobbling” and tRNA-34 Wobble and tRNA-37 Anticodon Loop Modifications in Evolution and Devolution of the Genetic Code

The genetic code evolved around the reading of the tRNA anticodon on the primitive ribosome, and tRNA-34 wobble and tRNA-37 modifications coevolved with the code. We posit that EF-Tu, the closing mechanism of the 30S ribosomal subunit, methylation of wobble U34 at the 5-carbon and suppression of wobbling at the tRNA-36 position were partly redundant and overlapping functions that coevolved to establish the code. The genetic code devolved in evolution of mitochondria to reduce the size of the tRNAome (all of the tRNAs of an organism or organelle). “Superwobbling” or four-way wobbling describes a major mechanism for shrinking the mitochondrial tRNAome. In superwobbling, unmodified wobble tRNA-U34 can recognize all four codon wobble bases (A, G, C and U), allowing a single unmodified tRNA-U34 to read a 4-codon box. During code evolution, to suppress superwobbling in 2-codon sectors, U34 modification by methylation at the 5-carbon position appears essential. As expected, at the base of code evolution, tRNA-37 modifications mostly related to the identity of the adjacent tRNA-36 base. TRNA-37 modifications help maintain the translation frame during elongation.

RNP-world: The ultimate essence of life is a ribonucleoprotein process

The fundamental essence of life is based on process of interaction between nucleic acids and proteins. In a prebiotic world, amino acids, peptides, ions, and other metabolites acted in protobiotic routes at the same time on which RNAs performed catalysis and self-replication. Nevertheless, it was only when nucleic acids and peptides started to interact together in an organized process that life emerged. First, the ignition was sparked with the formation of a Peptidyl Transferase Center (PTC), possibly by concatenation of proto-tRNAs. This molecule that would become the catalytic site of ribosomes started a process of self-organization that gave origin to a protoorganism named FUCA, a ribonucleic ribosomal-like apparatus capable to polymerize amino acids. In that sense, we review hypotheses about the origin and early evolution of the genetic code. Next, populations of open biological systems named progenotes were capable of accumulating and exchanging genetic material, producing the first genomes. Progenotes then evolved in two paths: some presented their own ribosomes and others used available ribosomes in the medium to translate their encoded information. At some point, two different types of organisms emerged from populations of progenotes: the ribosome-encoding organisms (cells) and the capsid-encoding organisms (viruses).

Fitting the standard genetic code into its triplet table

Minimally evolved codes are constructed here; these have randomly chosen standard genetic code (SGC) triplets, completed with completely random triplet assignments. Such "genetic codes" have not evolved, but retain SGC qualities. Retained qualities are basic, part of the underpinning of coding. For example, the sensitivity of coding to arbitrary assignments, which must be < ∼10%, is intrinsic. Such sensitivity comes from the elementary combinatorial properties of coding and constrains any SGC evolution hypothesis. Similarly, assignment of last-evolved functions is difficult because of late kinetic phenomena, likely common across codes. Census of minimally evolved code assignments shows that shape and size of wobble domains controls the code's fit into a coding table, strongly shifting accuracy of codon assignments. Access to the SGC therefore requires a plausible pathway to limited randomness, avoiding difficult completion while fitting a highly ordered, degenerate code into a preset three-dimensional space. Three-dimensional late Crick wobble in a genetic code assembled by lateral transfer between early partial codes satisfies these varied, simultaneous requirements. By allowing parallel evolution of SGC domains, this origin can yield shortened evolution to SGC-level order and allow the code to arise in smaller populations. It effectively yields full codes. Less obviously, it unifies previously studied chemical, biochemical, and wobble order in amino acid assignment, including a stereochemical minority of triplet-amino acid associations. Finally, fusion of intermediates into the final SGC is credible, mirroring broadly accepted later cellular evolution.

Evolution of the genetic code

Diverse models have been advanced for the evolution of the genetic code. Here, models for tRNA, aminoacyl-tRNA synthetase (aaRS) and genetic code evolution were combined with an understanding of EF-Tu suppression of tRNA 3^rd anticodon position wobbling. The result is a highly detailed scheme that describes the placements of all amino acids in the standard genetic code. The model describes evolution of 6-, 4-, 3-, 2- and 1-codon sectors. Innovation in column 3 of the code is explained. Wobbling and code degeneracy are explained. Separate distribution of serine sectors between columns 2 and 4 of the code is described. We conclude that very little chaos contributed to evolution of the genetic code and that the pattern of evolution of aaRS enzymes describes a history of the evolution of the code. A model is proposed to describe the biological selection for the earliest evolution of the code and for protocell evolution.

Optimal Evolution of the Standard Genetic Code

The 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.