scholarly journals On the origin of the mitochondrial genetic code: Towards a unified mathematical framework for the management of genetic information

2012 ◽  
Author(s):  
Diego Luis Gonzalez ◽  
Simone Giannerini ◽  
Rodolfo Rosa
Keyword(s):  
Genetic Code ◽  
Genetic Information ◽  
Mathematical Framework ◽  
Mitochondrial Genetic Code

scholarly journals On the origin of degeneracy in the genetic code

2019 ◽  
Vol 9 (6) ◽  
pp. 20190038 ◽  
Author(s):  
D. L. Gonzalez ◽  
S. Giannerini ◽  
R. Rosa
Keyword(s):  
Genetic Code ◽  
Common Ancestor ◽  
Mathematical Framework ◽  
Last Universal Common Ancestor ◽  
Evolutionary Transitions ◽  
Genetic Codes ◽  
Mitochondrial Genetic Code ◽  
Symmetry Principles ◽  
Universal Common Ancestor ◽  
New Perspective

The degeneracy of amino acid coding is one of the most crucial and enigmatic aspects of the genetic code. Different theories about the origin of the genetic code have been developed. However, to date, there is no comprehensive hypothesis on the mechanism that might have generated the degeneracy as we observe it. Here, we provide a new theory that explains the origin of the degeneracy based only on symmetry principles. The approach allows one to describe exactly the degeneracy of the early code (progenitor of the genetic code of LUCA, the last universal common ancestor) which is hypothesized to have the same degeneracy as the present vertebrate mitochondrial genetic code. The theory is based upon the tessera code, that fits as the progenitor of the early code. Moreover, we describe in detail the possible evolutionary transitions implied by our theory. The approach is supported by a unified mathematical framework that accounts for the degeneracy properties of both nuclear and mitochondrial genetic codes. Our work provides a new perspective to the understanding of the origin of the genetic code and the roles of symmetry principles in the organization of genetic information.

scholarly journals Widespread use of the “ascidian” mitochondrial genetic code in tunicates

F1000Research ◽  
2020 ◽  
Vol 8 ◽  
pp. 2072
Author(s):  
Julien Pichon ◽  
Nicholas M. Luscombe ◽  
Charles Plessy
Keyword(s):  
Genetic Code ◽  
Stop Codon ◽  
Mitochondrial Protein ◽  
Sequence Alignments ◽  
Additional Species ◽  
Multiple Sequence ◽  
Oikopleura Dioica ◽  
Mitochondrial Genetic Code ◽  
Mitochondrial Sequences ◽  
Mitochondrial Code

Background: Ascidians, a tunicate class, use a mitochondrial genetic code that is distinct from vertebrates and other invertebrates. Though it has been used to translate the coding sequences from other tunicate species on a case-by-case basis, it is has not been investigated whether this can be done systematically. This is an important because a) some tunicate mitochondrial sequences are currently translated with the invertebrate code by repositories such as NCBI GenBank, and b) uncertainties about the genetic code to use can complicate or introduce errors in phylogenetic studies based on translated mitochondrial protein sequences. Methods: We collected publicly available nucleotide sequences for non-ascidian tunicates including appendicularians such as Oikopleura dioica, translated them using the ascidian mitochondrial code, and built multiple sequence alignments covering all tunicate classes. Results: All tunicates studied here appear to translate AGR codons to glycine instead of serine (invertebrates) or as a stop codon (vertebrates), as initially described in ascidians. Among Oikopleuridae, we suggest further possible changes in the use of the ATA (Ile → Met) and TGA (Trp → Arg) codons. Conclusions: We recommend using the ascidian mitochondrial code in automatic translation pipelines of mitochondrial sequences for all tunicates. Further investigation is required for additional species-specific differences.

Symmetries of the Degeneracy of the Vertebrate Mitochondrial Genetic Code in the Matrix Form

2010 ◽  
pp. 31-49
Author(s):  
Sergey Petoukhov ◽  
Matthew He
Keyword(s):  
Mathematical Modeling ◽  
Genetic Code ◽  
Matrix Form ◽  
Black And White ◽  
Mitochondrial Genetic Code ◽  
The Matrix

Symmetries of the degeneracy of the vertebrate mitochondrial genetic code in the mosaic matrix form of its presentation are described in this chapter. The initial black-and-white genomatrix of this code is reformed into a new mosaic matrix when internal positions in all triplets are permuted simultaneously. It is revealed unexpectedly that for all six variants of positional permutations in triplets (1-2-3, 2-3-1, 3-1-2, 1-3-2, 2-1-3, 3-2-1) the appropriate genetic matrices possess symmetrical mosaics of the code degeneracy. Moreover the six appropriate mosaic matrices in their binary presentation have the general non-trivial property of their “tetra-reproduction,” which can be utilized in particular for mathematical modeling of the phenomenon of the tetra-division of gametal cells in meiosis. Mutual interchanges of the genetic letters A, C, G, U in the genomatrices lead to new mosaic genomatrices, which possess similar symmetrical and tetra-reproduction properties as well.

scholarly journals The non-power model of the genetic code: a paradigm for interpreting genomic information

2016 ◽  
Vol 374 (2063) ◽  
pp. 20150062 ◽  
Author(s):  
Diego Luis Gonzalez ◽  
Simone Giannerini ◽  
Rodolfo Rosa
Keyword(s):  
Genetic Code ◽  
Power Model ◽  
Mathematical Framework ◽  
Genomic Information ◽  
Unified Framework ◽  
Hidden Symmetries ◽  
Protein Coding ◽  
The Core ◽  
Domains Of Life ◽  
Mitochondrial Code

In this article, we present a mathematical framework based on redundant (non-power) representations of integer numbers as a paradigm for the interpretation of genomic information. The core of the approach relies on modelling the degeneracy of the genetic code. The model allows one to explain many features and symmetries of the genetic code and to uncover hidden symmetries. Also, it provides us with new tools for the analysis of genomic sequences. We review briefly three main areas: (i) the Euplotid nuclear code, (ii) the vertebrate mitochondrial code, and (iii) the main coding/decoding strategies used in the three domains of life. In every case, we show how the non-power model is a natural unified framework for describing degeneracy and deriving sound biological hypotheses on protein coding. The approach is rooted on number theory and group theory; nevertheless, we have kept the technical level to a minimum by focusing on key concepts and on the biological implications.

scholarly journals Genetic code and number theory

2016 ◽  
Vol 14 (3) ◽  
pp. 225-241 ◽  
Author(s):  
Branko Dragovich
Keyword(s):  
Number Theory ◽  
Genetic Code ◽  
21St Century ◽  
Genetic Information ◽  
Life Science ◽  
Theoretical Approaches ◽  
Living Organisms ◽  
The Universe

Living organisms are the most complex, interesting and significant objects regarding all substructures of the universe. Life science is regarded as a science of the 21st century and one can expect great new discoveries in the near futures. This article contains an introductory brief review of genetic information, its coding and translation of genes to proteins through the genetic code. Some theoretical approaches to the modelling of the genetic code are presented. In particular, connection of the genetic code with number theory is considered and the role of p-adic numbers is underlined.

scholarly journals Widespread use of the “ascidian” mitochondrial genetic code in tunicates

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 2072 ◽  
Author(s):  
Julien Pichon ◽  
Nicholas M. Luscombe ◽  
Charles Plessy
Keyword(s):  
Genetic Code ◽  
Stop Codon ◽  
Mitochondrial Protein ◽  
Sequence Alignments ◽  
Additional Species ◽  
Multiple Sequence ◽  
Oikopleura Dioica ◽  
Mitochondrial Genetic Code ◽  
Mitochondrial Sequences ◽  
Mitochondrial Code

Background: Ascidians, a tunicate class, use a mitochondrial genetic code that is distinct from vertebrates and other invertebrates. Though it has been used to translate the coding sequences from other tunicate species on a case-by-case basis, it is has not been investigated whether this can be done systematically. This is an important because a) some tunicate mitochondrial sequences are currently translated with the invertebrate code by repositories such as NCBI GenBank, and b) uncertainties about the genetic code to use can complicate or introduce errors in phylogenetic studies based on translated mitochondrial protein sequences. Methods: We collected publicly available nucleotide sequences for non-ascidian tunicates including appendicularians such as Oikopleura dioica, translated them using the ascidian mitochondrial code, and built multiple sequence alignments covering all tunicate classes. Results: All tunicates studied here appear to translate AGR codons to glycine instead of serine (invertebrates) or as a stop codon (vertebrates), as initially described in ascidians. Among Oikopleuridae, we suggest further possible changes in the use of the ATA (Ile → Met) and TGA (Trp → Arg) codons. Conclusions: We recommend using the ascidian mitochondrial code in automatic translation pipelines of mitochondrial sequences for all tunicates. Further investigation is required for additional species-specific differences.

Linear codes and the mitochondrial genetic code

Biosystems ◽  
2019 ◽  
Vol 184 ◽  
pp. 103990
Author(s):  
Elena Fimmel ◽  
Lutz Strüngmann
Keyword(s):  
Genetic Code ◽  
Linear Codes ◽  
Mitochondrial Genetic Code
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