Pathways of Genetic Code Evolution in Ancient and Modern Organisms

  title={Pathways of Genetic Code Evolution in Ancient and Modern Organisms},
  author={Supratim Sengupta and Paul G. Higgs},
  journal={Journal of Molecular Evolution},
There have been two distinct phases of evolution of the genetic code: an ancient phase—prior to the divergence of the three domains of life, during which the standard genetic code was established—and a modern phase, in which many alternative codes have arisen in specific groups of genomes that differ only slightly from the standard code. Here we discuss the factors that are most important in these two phases, and we argue that these are substantially different. In the modern phase, changes are… 

Origin and Evolution of the Universal Genetic Code.

Phylogenetic analysis of translation system components, in particular aminoacyl-tRNA synthetases, shows that, at a stage of evolution when the translation system had already attained high fidelity, the correspondence between amino acids and cognate codons was determined by recognition of amino acids by RNA molecules, i.e., proto-tRNAs.

Evolutionary instability of CUG-Leu in the genetic code of budding yeasts

It is proposed that the three parallel reassignments of CUG were not driven by natural selection in favor of their effects on the proteome, but by selection to eliminate the ancestral tRNALeu(CAG).

Finite population analysis of the effect of horizontal gene transfer on the origin of an universal and optimal genetic code

This work examines a collective evolution model of genetic code origin that allows for unconstrained horizontal transfer of genetic elements within a finite population of sequences each of which is associated with a genetic code selected from a pool of primordial codes.

Observations and perspectives on the prebiotic sequence evolution

A prebiotic picture of the triplex nucleic acid evolution is proposed to explain theorigin of the genetic code, where the transition from disorder to order in the origin of life might be due to the increasing stabilities of triplex base pairs.

Rooted tRNAomes and evolution of the genetic code

It is proposed that the initial product of the genetic code may have been short chain polyglycine to stabilize protocells and the sectoring-degeneracy hypothesis is proposed, which describes how anticodons were allotted in evolution.

What Froze the Genetic Code?

A potential explanation to the reason why the Genetic Code has remained mostly stable for over three billion years is offered, and some of the mechanisms that allow species to overcome the intrinsic functional limitations of the protein synthesis machinery are discussed.

Finite population analysis of the effect of horizontal gene transfer on the origin of an universal and optimal genetic code

Simulation results reveal the conditions under which sharing of coding innovations through horizontal transfer of genetic elements may have facilitated the emergence of a universal code having a structure similar to that of the SGC.

Model of Genetic Code Structure Evolution under Various Types of Codon Reading

The simulation show that the unambiguous SGC could emerged from a code with a lower level of ambiguity and the number of tRNAs increased during the evolution.

Frozen Accident Pushing 50: Stereochemistry, Expansion, and Chance in the Evolution of the Genetic Code

This work outlines an experimentally testable scenario for the evolution of the code that combines a distinct version of the stereochemical hypothesis, in which amino acids are recognized via unique sites in the tertiary structure of proto-tRNAs, rather than by anticodons, and the frozen accident.



The Hypothesis that the Genetic Code Originated in Coupled Synthesis of Proteins and the Evolutionary Predecessors of Nucleic Acids in Primitive Cells

The hypothesis that the earliest predecessor of the nucleic acids was a β-linked polyester made from malic acid, a highly conserved metabolite in the carboxylic acid cycles, is advanced and reconciles the “genetics first” and “metabolism first’ approaches to the origin of life.

Two Perspectives on the Origin of the Standard Genetic Code

Two perspectives on code origin are provided by carrying out simulations of code-sequence coevolution in finite populations with the aim of examining how the standard genetic code may have evolved from more primitive code(s) encoding a small number of amino acids.

Driving change: the evolution of alternative genetic codes.

Revisiting the Physico-Chemical Hypothesis of Code Origin: An Analysis Based on Code-Sequence Coevolution in a Finite Population

It is found that the composition of the code population affects the code fixation probability, which suggests that physico-chemical optimization may not be the sole driving force in ensuring the emergence of the standard genetic code.

On the Evolution of Redundancy in Genetic Codes

The results suggest that various omnipresent phenomena that distribute codons over sites with different selective requirementspredispose the evolution of redundancy and of reduced amino acid diversity in genetic codes.

Mitochondrial Genetic Codes Evolve to Match Amino Acid Requirements of Proteins

An analysis of 24 phylogenetically independent codon reassignments in mitochondria strongly suggests that mitochondrial genetic codes evolve to match the amino acid requirements of proteins.

Evolution of the Genetic Code by Incorporation of Amino Acids that Improved or Changed Protein Function

  • B. Francis
  • Biology
    Journal of Molecular Evolution
  • 2013
Based on an analysis of amino acid function in proteins, an evolutionary mechanism for expansion of the genetic code is described in which individual coded amino acids were replaced by new amino acids that used nonsense codons differing by one base change from the sense codons previously used.

Unassigned Codons, Nonsense Suppression, and Anticodon Modifications in the Evolution of the Genetic Code

It is shown that the phenomenon of nonsense suppression as observed in current organisms allows for a scenario in which many unassigned codons persisted throughout most of the evolutionary development of the code and that incorporation of anticodon modifications at a late stage is feasible.

Genetic code development by stop codon takeover.

A Unified Model of Codon Reassignment in Alternative Genetic Codes

This work presents a new framework for codon reassignment that incorporates two previously proposed mechanisms (codon disappearance and ambiguous intermediate) and introduces two further mechanisms (unassigned codon and compensatory change).