scholarly journals Origin and evolution of the genetic code: The universal enigma

IUBMB Life ◽  
2009 ◽  
Vol 61 (2) ◽  
pp. spcone-spcone
Author(s):  
Eugene V. Koonin ◽  
Artem S. Novozhilov
Keyword(s):  
Genetic Code ◽  
Origin And Evolution

scholarly journals Origin and evolution of the genetic code: The universal enigma

IUBMB Life ◽  
2009 ◽  
Vol 61 (2) ◽  
pp. 99-111 ◽  
Author(s):  
Eugene V. Koonin ◽  
Artem S. Novozhilov
Keyword(s):  
Genetic Code ◽  
Origin And Evolution

scholarly journals Standard genetic code: p-adic modelling, nucleon balances and selfsimilarity

2016 ◽  
Vol 14 (3) ◽  
pp. 275-298 ◽  
Author(s):  
Natasa Misic
Keyword(s):  
Amino Acid ◽  
Genetic Code ◽  
Driving Forces ◽  
Standard Genetic Code ◽  
Origin And Evolution ◽  
Novel Approach ◽  
Nucleon Number ◽  
The One ◽  
Mitochondrial Code ◽  
Rna And Dna

This paper represents the preliminary results and conclusions on the one of fundamental questions of the genetic code related to the underlying selective mechanisms involved in its origin and evolution, in particular their hypothetical different nature, originally considered in [1,2,3]. A novel approach is introduced, based on known arithmetic regularities inside the genetic code, determined by the nucleon balances of amino acids and their divisibility by the decimal number 37 [4]. As a parameter of the genetic code systematization is introduced an aggregate nucleon number of amino acid and cognate codon, while divisibility test is carried out not only by the number 37, but also by 13.7, the selfsimilarity constant of decimal scaling [5]. Relevant nucleon sums were obtained for the most prominent divisions of the standard genetic code (SGC) according to p-adic model of the vertebrate mitochondrial code (VMC) in [6]. The nucleon number divisibility pattern of 37 and 13.7 for the RNA and DNA codon space, as well as for the amino acid space is also analyzed. The obtained results, particularly a general higher divisibility of the nucleon sums by the numbers 37 and 13.7 in SGC than in VMC, as well as a correspondence between the nucleon number divisibility pattern of both the RNA codon space and the amino acid space of SGC, how separately so conjointly, with the code degeneracy pattern, suggest some conclusions: support the hypothesis [1,2,3,7] that the selective driving forces acting during an emergence (an ancient phase) and an evolution (a modern phase) of the genetic code are different, imply the existence of an environmental-dependent stereochemical mechanism throughout the entire period of the genetic code emergence and support a mineral-mediated origin of the genetic code [7,8].

The Origin and Evolution of the Genetic Code

1981 ◽  
pp. 431-437 ◽  
Author(s):  
Alain Figureau ◽  
Jean-Michel Labouygues
Keyword(s):  
Genetic Code ◽  
Origin And Evolution

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

2017 ◽  
Author(s):  
Eugene Koonin
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Tertiary Structure ◽  
Life Forms ◽  
Translation System ◽  
Default Theory ◽  
Origin And Evolution ◽  
Francis Crick ◽  
Standard Code ◽  
Early Translation

Nearly 50 years ago, Francis Crick propounded the frozen accident scenario for the evolution of the genetic code along with the hypothesis that the early translation system consisted primarily of RNA. Under the frozen accident perspective, the code is universal among modern life forms because any change in codon assignment would be highly deleterious. The frozen accident can be considered the default theory of code evolution because it does not imply any specific interactions between amino acids and the cognate codons or anticodons, or any particular properties of the code. The subsequent 49 years of code studies have elucidated notable features of the standard code, such as high robustness to errors, but failed to develop a compelling explanation for codon assignments. In particular, stereochemical affinity between amino acids and the cognate codons or anticodons does not seem to account for the origin and evolution of the code. Here I expand Crick’s hypothesis on RNA-only translation system by presenting evidence that this early translation already attained high fidelity that allowed protein evolution. I outline 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, expansion of the code via proto-tRNA duplication and the frozen accident.

The Origin and Evolution of the Genetic Code

1994 ◽  
Vol 170 (4) ◽  
pp. 359-365 ◽  
Author(s):  
Pierre Béland ◽  
T.F.H. Allen
Keyword(s):  
Genetic Code ◽  
Origin And Evolution

scholarly journals Transcript Regulation of the Recoded Archaeal α-l-Fucosidase In Vivo

Molecules ◽  
2021 ◽  
Vol 26 (7) ◽  
pp. 1861
Author(s):  
Federica De Lise ◽  
Roberta Iacono ◽  
Andrea Strazzulli ◽  
Rosa Giglio ◽  
Nicola Curci ◽  
...  
Keyword(s):  
Genetic Code ◽  
Growth Conditions ◽  
Point Of View ◽  
Translation Efficiency ◽  
Origin And Evolution ◽  
New Information ◽  
Evolutionary Advantage ◽  
Life On Earth ◽  
First Time

Genetic decoding is flexible, due to programmed deviation of the ribosomes from standard translational rules, globally termed “recoding”. In Archaea, recoding has been unequivocally determined only for termination codon readthrough events that regulate the incorporation of the unusual amino acids selenocysteine and pyrrolysine, and for −1 programmed frameshifting that allow the expression of a fully functional α-l-fucosidase in the crenarchaeon Saccharolobus solfataricus, in which several functional interrupted genes have been identified. Increasing evidence suggests that the flexibility of the genetic code decoding could provide an evolutionary advantage in extreme conditions, therefore, the identification and study of interrupted genes in extremophilic Archaea could be important from an astrobiological point of view, providing new information on the origin and evolution of the genetic code and on the limits of life on Earth. In order to shed some light on the mechanism of programmed −1 frameshifting in Archaea, here we report, for the first time, on the analysis of the transcription of this recoded archaeal α-l-fucosidase and of its full-length mutant in different growth conditions in vivo. We found that only the wild type mRNA significantly increased in S. solfataricus after cold shock and in cells grown in minimal medium containing hydrolyzed xyloglucan as carbon source. Our results indicated that the increased level of fucA mRNA cannot be explained by transcript up-regulation alone. A different mechanism related to translation efficiency is discussed.

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