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A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code.

Higgs PG - Biol. Direct (2009)

Bottom Line: Hence, the effects of translational error are minimized with respect to randomly reshuffled codes.As a result, the properties of the amino acids in the final code retain a four-column pattern that is a relic of the earliest stages of code evolution.Nevertheless, the code that results is one in which translational error is minimized.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Physics and Astronomy, McMaster University, Hamilton, Ontario L8S 4M1, Canada. higgsp@mcmaster.ca

ABSTRACT

Background: The arrangement of the amino acids in the genetic code is such that neighbouring codons are assigned to amino acids with similar physical properties. Hence, the effects of translational error are minimized with respect to randomly reshuffled codes. Further inspection reveals that it is amino acids in the same column of the code (i.e. same second base) that are similar, whereas those in the same row show no particular similarity. We propose a 'four-column' theory for the origin of the code that explains how the action of selection during the build-up of the code leads to a final code that has the observed properties.

Results: The theory makes the following propositions. (i) The earliest amino acids in the code were those that are easiest to synthesize non-biologically, namely Gly, Ala, Asp, Glu and Val. (ii) These amino acids are assigned to codons with G at first position. Therefore the first code may have used only these codons. (iii) The code rapidly developed into a four-column code where all codons in the same column coded for the same amino acid: NUN = Val, NCN = Ala, NAN = Asp and/or Glu, and NGN = Gly. (iv) Later amino acids were added sequentially to the code by a process of subdivision of codon blocks in which a subset of the codons assigned to an early amino acid were reassigned to a later amino acid. (v) Later amino acids were added into positions formerly occupied by amino acids with similar properties because this can occur with minimal disruption to the proteins already encoded by the earlier code. As a result, the properties of the amino acids in the final code retain a four-column pattern that is a relic of the earliest stages of code evolution.

Conclusion: The driving force during this process is not the minimization of translational error, but positive selection for the increased diversity and functionality of the proteins that can be made with a larger amino acid alphabet. Nevertheless, the code that results is one in which translational error is minimized. We define a cost function with which we can compare the fitness of codes with varying numbers of amino acids, and a barrier function, which measures the change in cost immediately after addition of a new amino acid. We show that the barrier is positive if an amino acid is added into a column with dissimilar properties, but negative if an amino acid is added into a column with similar physical properties. Thus, natural selection favours the assignment of amino acids to the positions that they occupy in the final code.

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Early structure of the code predicted by coevolution theory (stage b of Di Giulio and Medugno [56]).
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Figure 6: Early structure of the code predicted by coevolution theory (stage b of Di Giulio and Medugno [56]).

Mentions: The coevolution theory proposes that when each new amino acid was added to the code, it took over some of the codons that were previously assigned to its precursor. If one accepts that this is true for all amino acids, and if all the biosynthesis pathways were the same then and they are now, then we can trace each amino acid back to its earliest precursor and deduce the structure of the genetic code at the time when only the earliest precursor amino acids were present. This is done in most detail by Di Giulio and Medugno [56]. The resulting code is shown in Figure 6. This figure corresponds to stage b of Figure 1 of [56]. These authors consider one prior stage in which the Val codons in Figure 6 were assigned to Ala. However, a more recent version shown in Figure 4 of [22], has Val in the position shown. Therefore stage b seems like a good code with which to begin according the coevolution theory.


A four-column theory for the origin of the genetic code: tracing the evolutionary pathways that gave rise to an optimized code.

Higgs PG - Biol. Direct (2009)

Early structure of the code predicted by coevolution theory (stage b of Di Giulio and Medugno [56]).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2689856&req=5

Figure 6: Early structure of the code predicted by coevolution theory (stage b of Di Giulio and Medugno [56]).
Mentions: The coevolution theory proposes that when each new amino acid was added to the code, it took over some of the codons that were previously assigned to its precursor. If one accepts that this is true for all amino acids, and if all the biosynthesis pathways were the same then and they are now, then we can trace each amino acid back to its earliest precursor and deduce the structure of the genetic code at the time when only the earliest precursor amino acids were present. This is done in most detail by Di Giulio and Medugno [56]. The resulting code is shown in Figure 6. This figure corresponds to stage b of Figure 1 of [56]. These authors consider one prior stage in which the Val codons in Figure 6 were assigned to Ala. However, a more recent version shown in Figure 4 of [22], has Val in the position shown. Therefore stage b seems like a good code with which to begin according the coevolution theory.

Bottom Line: Hence, the effects of translational error are minimized with respect to randomly reshuffled codes.As a result, the properties of the amino acids in the final code retain a four-column pattern that is a relic of the earliest stages of code evolution.Nevertheless, the code that results is one in which translational error is minimized.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Physics and Astronomy, McMaster University, Hamilton, Ontario L8S 4M1, Canada. higgsp@mcmaster.ca

ABSTRACT

Background: The arrangement of the amino acids in the genetic code is such that neighbouring codons are assigned to amino acids with similar physical properties. Hence, the effects of translational error are minimized with respect to randomly reshuffled codes. Further inspection reveals that it is amino acids in the same column of the code (i.e. same second base) that are similar, whereas those in the same row show no particular similarity. We propose a 'four-column' theory for the origin of the code that explains how the action of selection during the build-up of the code leads to a final code that has the observed properties.

Results: The theory makes the following propositions. (i) The earliest amino acids in the code were those that are easiest to synthesize non-biologically, namely Gly, Ala, Asp, Glu and Val. (ii) These amino acids are assigned to codons with G at first position. Therefore the first code may have used only these codons. (iii) The code rapidly developed into a four-column code where all codons in the same column coded for the same amino acid: NUN = Val, NCN = Ala, NAN = Asp and/or Glu, and NGN = Gly. (iv) Later amino acids were added sequentially to the code by a process of subdivision of codon blocks in which a subset of the codons assigned to an early amino acid were reassigned to a later amino acid. (v) Later amino acids were added into positions formerly occupied by amino acids with similar properties because this can occur with minimal disruption to the proteins already encoded by the earlier code. As a result, the properties of the amino acids in the final code retain a four-column pattern that is a relic of the earliest stages of code evolution.

Conclusion: The driving force during this process is not the minimization of translational error, but positive selection for the increased diversity and functionality of the proteins that can be made with a larger amino acid alphabet. Nevertheless, the code that results is one in which translational error is minimized. We define a cost function with which we can compare the fitness of codes with varying numbers of amino acids, and a barrier function, which measures the change in cost immediately after addition of a new amino acid. We show that the barrier is positive if an amino acid is added into a column with dissimilar properties, but negative if an amino acid is added into a column with similar physical properties. Thus, natural selection favours the assignment of amino acids to the positions that they occupy in the final code.

Show MeSH