The origin of the genetic code: theories and their relationships, a review

Giulio, Massimo Di

doi:10.1016/j.biosystems.2004.11.005

Cited by 131 publications

(73 citation statements)

References 126 publications

(194 reference statements)

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“…Di Giulio (2005), in a review on the theories of the origin and evolution of the genetic code, distinguishes two basic alternatives. The stereochemical theory claims that the origin of the genetic code must lie in the stereochemical interactions between anticodons or codons and amino acids.…”

Section: Accepted Manuscriptmentioning

confidence: 99%

Study of the genetic code adaptability by means of a genetic algorithm

Santos¹,

Monteagudo²

2010

Journal of Theoretical Biology

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Cite this article as: José Santos and Ángel Monteagudo, Study of the genetic code adaptability by means of a genetic algorithm, Journal of Theoretical Biology, doi:10.1016Biology, doi:10. /j.jtbi.2010 This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting galley proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. AbstractWe used simulated evolution to study the adaptability level of the canonical geneticcode. An adapted genetic algorithm (GA) searches for optimal hypothetical codes.Adaptability is measured as the average variation of the hydrophobicity that the encoded amino acids undergo when errors or mutations are present in the codons of the hypothetical codes. Different types of mutations and point mutation rates that depend on codon base number are considered in this study. Previous works have used statistical approaches based on randomly generated alternative codes or have used local search techniques to determine an optimum value. In this work, we emphasize what can be concluded from the use of simulated evolution considering the results of previous works. The GA provides more information about the difficulty of the evolution of codes, without contradicting previous studies using statistical or engineering approaches. The GA also shows that, within the coevolution theory, the third base clearly improves the adaptability of the current genetic code.

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Section: Accepted Manuscriptmentioning

confidence: 99%

Study of the genetic code adaptability by means of a genetic algorithm

Santos¹,

Monteagudo²

2010

Journal of Theoretical Biology

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“…At least three different types of ideas are classically invoked (Knight et al 1999;Di Giulio 2005) to explain the evolution of the genetic code-they are actually not mutually exclusive and may all be true but correspond to different periods during this evolution. In the ''adaptation idea,'' the codon assignment problem is described as a typical optimization problem with an error minimization scheme stating: ''Near codons should encode similar amino acids.''…”

Section: Invasion Of the Codon Table: A Two-step Model?mentioning

confidence: 99%

“…A number of studies have assessed more quantitatively the importance of this criterion in understanding the genetic code (Freeland and Hurst 1998;Trinquier and Sanejouand 1998). In the resulting physicochemical and ambiguity reduction theory (Sonneborn 1965;Woese 1965a;Di Giulio 2005) the presentday genetic code is seen as mainly the result of physicochemical forces (and, of course, natural selection). However, Wong made the point that the relationships between amino acids encoded by near codons more faithfully reflect known biosynthetic pathways rather than physicochemical similarities (Wong 1975).…”

Section: Invasion Of the Codon Table: A Two-step Model?mentioning

confidence: 99%

An asymmetric underlying rule in the assignment of codons: Possible clue to a quick early evolution of the genetic code via successive binary choices

Delarue¹

2006

RNA

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Aminoacyl-tRNA synthetases (aaRSs) are responsible for creating the pool of correctly charged aminoacyl-tRNAs that are necessary for the translation of genetic information (mRNA) by the ribosome. Each aaRS belongs to either one of only two classes with two different mechanisms of aminoacylation, making use of either the 29OH (Class I) or the 39OH (Class II) of the terminal A76 of the tRNA and approaching the tRNA either from the minor groove (29OH) or the major groove (39OH). Here, an asymmetric pattern typical of differentiation is uncovered in the partition of the codon repertoire, as defined by the mechanism of aminoacylation of each corresponding tRNA. This pattern can be reproduced in a unique cascade of successive binary decisions that progressively reduces codon ambiguity. The deduced order of differentiation is manifestly driven by the reduction of translation errors. A simple rule can be defined, decoding each codon sequence in its binary class, thereby providing both the code and the key to decode it. Assuming that the partition into two mechanisms of tRNA aminoacylation is a relic that dates back to the invention of the genetic code in the RNA World, a model for the assignment of amino acids in the codon table can be derived. The model implies that the stop codon was always there, as the codon whose tRNA cannot be charged with any amino acid, and makes the prediction of an ultimate differentiation step, which is found to correspond to the codon assignment of the 22nd amino acid pyrrolysine in archaebacteria.

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“…'Stereochemical theory' (Crick 1968) suggests that aminoacylation of adapters has not been random before the emergence of peptide synthesis (reviewed in (Di Giulio 2005)). It proposes a stereochemical relationship between amino acids and corresponding codons and/or anticodons.…”

Section: Discussionmentioning

confidence: 99%

Hypothesis: Emergence of Translation as a Result of RNA Helicase Evolution

Zenkin

2012

J Mol Evol

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The origin of translation and the genetic code is one of the major mysteries of evolution. The advantage of templated protein synthesis could have been achieved only when the translation apparatus had already become very complex. This means that the translation machinery, as we know it today, must have evolved towards some different essential function that subsequently sub-functionalised into templated protein synthesis. The hypothesis presented here proposes that translation originated as the result of evolution of a primordial RNA helicase, which has been essential for preventing dying out of the RNA organism in sterile double-stranded form. This hypothesis emerges because modern ribosome possesses RNA helicase activity that likely dates back to the RNA world. I hypothesise that codon-anticodon interactions of tRNAs with mRNA evolved as a mechanism used by RNA helicase, the predecessor of ribosomes, to melt RNA duplexes. In this scenario, peptide bond formation emerged to drive unidirectional movement of the helicase via a molecular ratchet mechanism powered by Brownian motion. I propose that protein synthesis appeared as a side product of helicase activity. The first templates for protein synthesis were functional RNAs (ribozymes) that were unwound by the helicase, and the first synthesised proteins were of random or non-sense sequence. I further suggest that genetic code emerged to avoid this randomness. The initial genetic code thus emerged as an assignment of amino acids to codons according to the sequences of the pre-existing RNAs to take advantage of the side products of RNA helicase function.

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The origin of the genetic code: theories and their relationships, a review

Cited by 131 publications

References 126 publications

Study of the genetic code adaptability by means of a genetic algorithm

Study of the genetic code adaptability by means of a genetic algorithm

An asymmetric underlying rule in the assignment of codons: Possible clue to a quick early evolution of the genetic code via successive binary choices

Hypothesis: Emergence of Translation as a Result of RNA Helicase Evolution

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