Stereochemical Relationship Between Coding Triplets and Amino-Acids

Pelc, S. R.; Welton, M. G. E.

doi:10.1038/209868a0

Cited by 118 publications

(43 citation statements)

References 7 publications

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“…The first one assumes some structural and physicochemical relationships and interactions between stretches of RNA (codons, anticodons, reversed codons, codon-anticodon double helices etc.) and coded amino acids [4,5,6]. So far, a wellconfirmed relationship has been found for seven of eight amino acids (see for review: [7]).…”

Section: Introductionmentioning

confidence: 89%

Optimisation of Asymmetric Mutational Pressure and Selection Pressure Around the Universal Genetic Code

Biecek¹,

Mackiewicz²,

Kiraga³

et al. 2008

Computational Science – ICCS 2008

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Abstract.One of hypotheses explaining the origin of the genetic code assumes that its evolution has minimised the deleterious effects of mutations in coded proteins. To estimate the level of such optimization, we calculated optimal codes for genes located on differently replicating DNA strands separately assuming the rate of amino acid substitutions in proteins as a measure of code's susceptibility to errors. The optimal code for genes located on one DNA strand was simultaneously worse than the universal code for the genes located on the other strand. Furthermore, we generated 20 million random codes of which only 23 were better than the universal one for genes located on both strands simultaneously while about two orders of magnitude more codes were better for each of the two strands separately. The result indicates that the existing universal code, the mutational pressure, the codon and amino acid compositions are highly optimised for the both differently replicating DNA strands.

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Section: Introductionmentioning

confidence: 89%

Optimisation of Asymmetric Mutational Pressure and Selection Pressure Around the Universal Genetic Code

Biecek¹,

Mackiewicz²,

Kiraga³

et al. 2008

Computational Science – ICCS 2008

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show abstract

“…An alternative hypothesis is that the apparent load minimization may be largely an artefact, produced by what might be considered`historical' forces (Nirenberg et al 1963;Pelc & Welton 1966;Dillon 1973;Wong 1975Wong , 1976Wong , 1980Wong , 1981Wong , 1988Wong & Bronskill 1979;Taylor & Coates 1989). Typically, such arguments propose that the primordial genetic code contained fewer than the 20 amino acids seen today (i.e.…”

Section: Introductionmentioning

confidence: 99%

Load minimization of the genetic code: history does not explain the pattern

Freeland

Hurst

1998

Proc. R. Soc. Lond. B

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The average e¡ect of errors acting on a genetic code (the change in amino-acid meaning resulting from point mutation and mistranslation) may be quanti¢ed as its`load'. The natural genetic code shows a clear property of minimizing this load when compared against randomly generated variant codes. Two hypotheses may be considered to explain this property. First, it is possible that the natural code is the result of selection to minimize this load. Second, it is possible that the property is an historical artefact. It has previously been reported that amino acids that have been assigned to codons starting with the same base come from the same biosynthetic pathway. This probably re£ects the manner in which the code evolved from a simpler code, and says more about the physicochemical mechanisms of code assembly than about selection. The apparent load minimization of the code may therefore follow as a consequence of the fact that the code could not have evolved any other way than to allow biochemically related amino acids to have related codons. Here then, we ask whether this`historical' force alone can explain the e¤ciency of the natural code in minimizing the e¡ects of error. We therefore compare the error-minimizing ability of the natural code with that of alternative codes which, rather than being a random selection, are restricted such that amino acids from the same biochemical pathway all share the same ¢rst base. We ¢nd that although on average the restricted set of codes show a slightly higher e¤ciency than random ones, the real code remains extremely e¤cient relative to this subset p 0.0003. This indicates that for the most part historical features do not explain the load-minimization property of the natural code. The importance of selection is further supported by the ¢nding that the natural code's e¤ciency improves relative to that of historically related codes after allowance is made for realistic mutational and mistranslational biases. Once mistranslational biases have been considered, fewer than four per 100 000 alternative codes are better than the natural code.

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“…The two main alternatives are stereochemical predetermination of the genetic code through intrinsic affinities of the various amino acids with distinct components of the translation apparatus (e.g. Woese 1965bWoese , 1967Woese , 1973Pelc & Welton 1966;Woese et al 1966;Juncgk 1978;Shimizu 1982;Lacey & Mullins 1983;Yarus 2000, and references therein) and coevolution with amino acid biosynthesis wherein the code vocabulary of amino acids is thought to have expanded through the reassignment of codons from amino acids to their biosynthetic products (e.g. Wong 1975Wong , 1980Taylor & Coates 1989;Di Giulio 1995;Di Giulio & Medugno 1999, and references therein).…”

Section: Introductionmentioning

confidence: 99%

No accident: genetic codes freeze in error–correcting patterns of the standard genetic code

Ardell

Sella

2002

Phil. Trans. R. Soc. Lond. B

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The standard genetic code poses a challenge in understanding the evolution of information processing at a fundamental level of biological organization. Genetic codes are generally coadapted with, or 'frozen' by, the protein-coding genes that they translate, and so cannot easily change by natural selection. Yet the standard code has a significantly non-random pattern that corrects common errors in the transmission of information in protein-coding genes. Because of the freezing effect and for other reasons, this pattern has been proposed not to be due to selection but rather to be incidental to other evolutionary forces or even entirely accidental.We present results from a deterministic population genetic model of code-message coevolution. We explicitly represent the freezing effect of genes on genetic codes and the perturbative effect of changes in genetic codes on genes. We incorporate characteristic patterns of mutation and translational error, namely, transition bias and positional asymmetry, respectively. Repeated selection over small successive changes produces genetic codes that are substantially, but not optimally, error correcting. In particular, our model reproduces the error-correcting patterns of the standard genetic code. Aspects of our model and results may be applicable to the general problem of adaptation to error in other natural information-processing systems.

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Stereochemical Relationship Between Coding Triplets and Amino-Acids

Cited by 118 publications

References 7 publications

Optimisation of Asymmetric Mutational Pressure and Selection Pressure Around the Universal Genetic Code

Optimisation of Asymmetric Mutational Pressure and Selection Pressure Around the Universal Genetic Code

Load minimization of the genetic code: history does not explain the pattern

No accident: genetic codes freeze in error–correcting patterns of the standard genetic code

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