The origins of the genetic code

Dillon, Lawrence S.

doi:10.1007/bf02859159

Cited by 58 publications

(30 citation statements)

References 102 publications

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“…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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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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“…where 6 is small for small impact and large for large impact, but cannot exceed unity. Provided that 6 does not vary too greatly for different new amino acids, comparison of Eqs.…”

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confidence: 99%

“…Provided that 6 does not vary too greatly for different new amino acids, comparison of Eqs. 2 and 3 indicates that the balance between the benefit provided by the improvement in variety and the resistance posed by the replacement noise need not vary much with N.…”

mentioning

confidence: 99%

“…Among extant organisms, the combined errors of transcription and translation do not exceed 0.0003, and the translation noise alone must be even less (14). Addition of yet another amino acid (N = 21) will encounter a stability quotient of 1.6 even if 6 is as low as 0.01. Consequently the entry of such extra amino acids as hydroxyproline and hydroxylysine into cellular proteins has to proceed by way of posttranslational modification of Pro and Lys residues rather than further subdivision of the Pro and Lys codon domains.…”

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confidence: 99%

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The evolution of a universal genetic code

Wong

1976

Proc. Natl. Acad. Sci. U.S.A.

115

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Some of the basic problems presented by the rapid evolution of a universal genetic code can be resolved by a mechanism of co-evolution of the code and the amino acids it serves. The genetic code of protein synthesis assigns 64 triplet codons to amino acids and translational signals. Since the coding is universal amongst all prokaryotic and eukaryotic species for which there is evidence (1), it appears to have remained unchanged throughout the course of biological evolution. The code therefore stands as a faithful record of the events which at an early stage of the development of life on this planet had led to its emergence, selection, and fixation. Nirenberg et al. (2) first observed that some of the amino acids coded for by contiguous codons in the code are physically or metabolically related to each other. Sonneborn (3) and Woese (4) suggested that the physical relatedness could have accumulated through natural selection by virtue of the protection it offered against lethal ,mutations or translational errors. As for the question of whether or not the metabolic relatedness might be traceable to the origin of the code, an important step toward its resolution was taken when Pelc (5) and Dillon (6) suggested that the distribution of the codons amongst the amino acids could have been guided by potential conversions between the amino acids. Unfortunately, the postulated conversions were entirely based on the structural relatedness of the amino acids, and contradicted many of the actual metabolic conversions already known to occur in organisms. All of these proposals postulated an evolutionary origin for the genetic code, but did not provide any unambiguous prediction of codon distribution that can be tested against the distribution found in the code. This untestability renders it impossible to define the extent to which the apparent physical or structural relatedness between neighboring amino acids in the code may be the consequence of chance rather than evolution. Given the abundance of such relatedness amongst amino acids, even completely random allocations of code words would not be devoid of all elements of relatedness.The co-evolution theory (7) attachment to tRNAs are well known; and the covalent transformation of an amino acid on the tRNA also finds illustration either enzymically in the formylation of Met-tRNA (8), or nonenzymically in the desulfurationof . Since the biosynthetic relationships between amino acids in present day organisms are clearly defined, predictions could be made on this basis regarding the distribution of the codons for both precursor-product and sibling pairs of amino acids in the code. The excellent fit between both types of predictions and the genetic code excludes chance and establishes evolution as the originator of the code. The necessity for nonevolutionary origins such as frozen accident or infection from an extraterrestrial source (10) is removed.Since evolution as we know it operates within the framework of a universal genetic code, the evolution of the universal cod...

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“…The coevolution model Degeneracy aside, there are other patterns observed in the table of the genetic code (for a good summary, see Figure 1 in Szathma´ry, 1999). Thus, amino acids adjacent in biosynthetic pathways cluster together in the code (Dillon, 1973;Jukes, 1973;Wong, 1975). Prebiotic chemistry on early Earth did not supply all 20 current protein amino acids (see part 5.2) and most likely some of them had a biosynthetic origin.…”

Section: An Expanding Codementioning

confidence: 99%

5. Prebiotic Chemistry – Biochemistry – Emergence of Life (4.4–2 Ga)

et al. 2006

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Abstract. This chapter is devoted to a discussion about the difficulties and even the impossibility to date the events that occurred during the transition from non-living matter to the first living cells. Nevertheless, the attempts to devise plausible scenarios accounting for the emergence of the main molecular devices and processes found in biology are presented including the role of nucleotides at early stages (RNA world). On the other hand, hypotheses on the development of early metabolisms, comEarth, Moon, and Planets (2006) 98: 153-203 Ó Springer 2006

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The origins of the genetic code

Cited by 58 publications

References 102 publications

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

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

The evolution of a universal genetic code

5. Prebiotic Chemistry – Biochemistry – Emergence of Life (4.4–2 Ga)

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