however, this altered tRNA
Ile
is also a much better substrate for MetRS than is for IleRS.
Thus, both the codon and the amino acid spe- cificity of this tRNA are changed by a single
posttranscriptional modification.’’
In this paper I have emphasized the codon – anticodon mapping, i.e. the assignment of codon
classes to
amino acids.
Recently, Davydov
1998 has proposed a set of rules to associate the amino acid end atoms ON and non-Onon-
N of 18 amino acids with codons containing weak bases AU. These rules correctly predict
all the codons in which the third base is non-re- dundant, that is, all the codons with doublets
B
1
B
2
in the set M
2
= AU, UU, UA, AA, GA,
CA, UG, AG, plus AC, GU and CU. The amino acids that, according Davydov’s rules, al-
low the correct association of codons are, I, M, L, F, Y, K, N, D, E, Q, H, C, W, T, V, R’, S’.
R’, S’ correspond to the ‘extra’ codons of R and S, respectively. Davydov’s rules give incorrect re-
sults for the codons of R, S and A. Glycine and proline were not considered in the analysis per-
formed by Davydov, for reasons explained in his article.
We have found an inverse of Davydov’s rules: 1. Codons of the form NAN + WCN have
amino acids with ON end atoms. 2. Codons of the form NUN + WGN have
amino acids with non-Onon-N end atoms. The exceptions being R and S.
3. Codons of the form SCN + SGN code for P, A, R, G. These amino acids either were
left out by Davydov or did not obey his rules.
Thus, it is seen that the amino acids beyond Davydov’s rules do not form a random set. All
of them have codons of the class SSN, which are the most stable codons Klump, 1993. With
the exception of arginine once more, the other three have no proper side-chain see Davydov’s
paper for further details. In Fig. 3 the amino acid recognized by the two classes of aminoacyl-
tRNA synthetases are ‘aligned’ with two amino acid groupings defined by, i end atom type and
ii codon type. It is clear from this figure, that the three ways of grouping amino acids are
strongly correlated.
6. Discussion
The model presented above is aimed to under- stand not just what now is, but the ways what
now is might plausibly be expected to have arisen Kauffman, 1993. It is based on two assump-
tions, the first is simply the hypothesis of a grad- ual change of the whole translation machinery. It
is difficult to imagine how changes in this vital part of the cell could have been possible other-
wise. The second follows from physical con- straints, which are consistent with measurements
of codon – anticodon Gibbs free-energy of interac- tion Klump and Maeder, 1991. Together with
the assumed initial conditions, they lead to a coherent picture of the code’s evolution, consis-
tent with extant evidence. Thus, we claim, the whole developmental process is imprinted in the
‘universal’ code not only the amino acid synthetic pathways, as assumed by Wong 1975, Wong
1976.
It is a current belief that, in present-day cells, the entire process of translation in the ribosome is
optimized towards
maximal efficiency.
That means towards the optimization of the average
translation rate of any one messenger being de- coded, with the highest fidelity. Thus, it is com-
monly accepted that speed and accuracy are the two basic parameters of the dynamics of the
ribosomal machinery Chavancy and Garel, 1981 and references therein. It is important to notice
that in this process the proper tRNA is selected only through codon – anticodon interactions, the
aminoacyl group does not take part Voet and Voet, 1995. It is natural to assume that this
optimization dominated the different stages of the code’s evolution, specified in our model, from
proto-cells to modern cells.
Klump and Maeder, 1991 developed the idea of a choice between speed and precision, to eluci-
date the relationship between the different evolu- tionary strategies followed by prokaryotes and
eukaryotes, as reflected in their different codon- usage and the codon – anticodon stability. It is
interesting to see the way the same concept could be applied to further developments of the present
model. According to these authors, ‘‘Choosing codons with the highest interaction Gibbs energies
is equivalent to choosing the most accurate pair- ing, especially with respect to the third wobble
position. The most accurate pairing is equivalent to the longest residence time for the codon – anti-
codon reading. This inevitably leads to the slowest transcription rate’’, and further, ‘‘...there are vari-
ations of this strategy, but the take-home message seems to be, eukaryotes go for precision. Their
prime aim is to keep the large genome as intact as possible’’.
As noticed by Woese 1965, it is clear that the early cell followed the same evolutionary strategy.
However, to picture later developments, following an optimization principle, it would be necessary
to consider both speed and accuracy. Translation error minimization alone is not enough.
7. Conclusions
