scholarly journals Concurrent origins of the genetic code and the homochirality of life, and the origin and evolution of biodiversity. Part II: Technical appendix

2015 ◽  
Author(s):  
Dirson Jian Li
Keyword(s):  
Genetic Code ◽  
Origin And Evolution ◽  
Technical Details

Here is Part II of my two-part series paper, which provides technical details and evidence for Part I of this paper (see “Concurrent origins of the genetic code and the homochirality of life, and the origin and evolution of biodiversity. Part I: Observations and explanations” on bioRxiv).

scholarly journals Concurrent origins of the genetic code and the homochirality of life, and the origin and evolution of biodiversity. Part I: Observations and explanations

2015 ◽  
Author(s):  
Dirson Jian Li
Keyword(s):  
Genetic Code ◽  
Early History ◽  
Mass Extinctions ◽  
Genome Sequences ◽  
Origin And Evolution ◽  
New Methods ◽  
Evolution Of Life ◽  
History Of ◽  
Technical Details ◽  
Recruitment Order

The post-genomic era has brought opportunities to bridge traditionally separate fields on early history of life. New methods promote a deeper understanding of the origin of biodiversity. Relative stabilities of base triplexes are able to regulate base substitutions in triplex DNAs. We constructed a roadmap based on such a regulation to explain concurrent origins of the genetic code and the homochirality of life. Based on the recruitment order of codons in the roadmap and the complete genome sequences, we reconstructed the three-domain tree of life. The Phanerozoic biodiversity curve has been reconstructed based on genomic, climatic and eustatic data; this result supports tectonic cause of mass extinctions. Our results indicate that chirality played a crucial role in the origin and evolution of life. Here is Part I of my two-part series paper; technical details are in Part II of my paper (see “Concurrent origins of the genetic code and the homochirality of life, and the origin and evolution of biodiversity. Part II: Technical appendix” on bioRxiv).

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.

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