Local conditions for global stability in the space of codons of the genetic code

Salinas, Dino G.; Gallardo, Mauricio O.; Osorio, Manuel I.

doi:10.1016/j.biosystems.2016.08.007

Cited by 5 publications

(3 citation statements)

References 15 publications

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“…Hence the error minimization theory of code evolution, under which the structure of the code is determined by selection for robustness to errors. Extensive quantitative analyses that employed cost functions differently derived from physico-chemical properties of amino acids have shown that the code is indeed highly resilient, with the probability to pick an equally robust random code being on the order of 10 −7 –10 −8 [14,15,61,62,63,64,65,66,67,68]. Obviously, however, among the ~10 84 possible random codes, there is a huge number with a higher degree of error minimization than the SGC.…”

Section: The Three Principal Scenarios Of the Code Origin And Evolmentioning

confidence: 99%

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

Koonin

2017

Life

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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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Section: The Three Principal Scenarios Of the Code Origin And Evolmentioning

confidence: 99%

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

Koonin

2017

Life

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show abstract

“…Hence the error minimization theory of code evolution, under which the structure of the code is determined by selection for robustness to errors. Extensive quantitative analyses that employed cost functions differently derived from physico-chemical properties of amino acids have shown that the code is indeed highly resilient, with the probability to pick an equally robust random code being on the order of 10 -7 -10 -8 [14,15,[61][62][63][64][65][66][67][68]. Obviously, however, among the ~10 84 possible random codes, there is a huge number with a higher degree of error minimization than the SGC.…”

Section: The Three Principal Scenarios Of the Code Origin And Evolutimentioning

confidence: 99%

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

Koonin¹

2017

Preprint

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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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“…Moreover, considering that sometimes code errors could be important for developing new cellular adaptive properties, perhaps genetic code evolution, rather than a way of optimizing stability, tended to optimize the balance between stability and adaptability. According to an evolutionary increase in stability, it has been found that the errors associated with the standard genetic code are considerably smaller than most random codes, although its achieved stability is not the best possible (Błażej et al 2018(Błażej et al , 2016Buhrman et al 2011;Freeland and Hurst 1998;Goldman 1993;Hurst 1991, 1999;Novozhilov et al 2007;Salinas et al 2016;Santos and Monteagudo 2010;Wnętrzak et al 2018Wnętrzak et al , 2019. The remarkable stability of the standard genetic code, besides being a driving force through the selection pressure, may have been a consequence of the expansion of the genetic code by mean of similar mechanism of codon assignments to physicochemically similar amino acids (Crick 1968;Koonin 2017).…”

Section: Introductionmentioning

confidence: 99%

Average and Standard Deviation of the Error Function for Random Genetic Codes with Standard Stop Codons

Salinas

2021

Acta Biotheor

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The origin of the genetic code has been attributed in part to an accidental assignment of codons to amino acids. Although several lines of evidence indicate the subsequent expansion and improvement of the genetic code, the hypothesis of Francis Crick concerning a frozen accident occurring at the early stage of genetic code evolution is still widely accepted. Considering Crick's hypothesis, mathematical descriptions of hypothetical scenarios involving a huge number of possible coexisting random genetic codes could be very important to explain the origin and evolution of a selected genetic code. This work aims to contribute in this regard, that is, it provides a theoretical framework in which statistical parameters of error functions are calculated. Given a genetic code and an amino acid property, the functional code robustness is estimated by means of a known error function. In this work, using analytical calculations, general expressions for the average and standard deviation of the error function distributions of completely random codes with standard stop codons were obtained. As a possible biological application of these results, any set of amino acids and any pure or mixed amino acid properties can be used in the calculations, such that, in case of having to select a set of amino acids to create a genetic code, possible advantages of natural selection of the genetic codes could be discussed.

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Local conditions for global stability in the space of codons of the genetic code

Cited by 5 publications

References 15 publications

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

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

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

Average and Standard Deviation of the Error Function for Random Genetic Codes with Standard Stop Codons

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