Dual functions of codons in the genetic code

Abstract

The discovery of the genetic code provided one of the basic foundations of modern molecular biology. Most organisms use the same genetic language, but there are also well-documented variations representing codon reassignments within specific groups of organisms (such as ciliates and yeast) or organelles (such as plastids and mitochondria). In addition, duality in codon function is known in the use of AUG in translation initiation and methionine insertion into internal protein positions as well as in the case of selenocysteine and pyrrolysine insertion (encoded by UGA and UAG, respectively) in competition with translation termination. Ambiguous meaning of CUG in coding for serine and leucine is also known. However, a recent study revealed that codons in any position within the open reading frame can serve a dual function and that a change in codon meaning can be achieved by availability of a specific type of RNA stem-loop structure in the 3'-untranslated region. Thus, duality of codon function is a more widely used feature of the genetic code than previously known, and this observation raises the possibility that additional recoding events and additional novel features have evolved in the genetic code.

Figure 1. The genetic code and its variations

The figure is available in color in the online publication. The genetic code is shown in the circular form, with known alternative meanings indicated outside the circle. Differences with the standard genetic code are shown as follows: red for mitochondrial, blue for ciliate and Euplotid nuclear code, and orange for the ambiguous yeast nuclear code. Sec and Pyl are shown in black.

Figure 2. Selenocysteine incorporation machinery

The figure is available in color in the online publication. The mechanism of Sec biosynthesis and incorporation into selenoproteins is shown and discussed in the text. Further discussion and identification of the various components involved in Sec biosynthesis are presented elsewhere (Xu et al, 2007).

Figure 3. Horizontal gene transfer of the pyrrolysine trait

The figure is available in color in the online publication. The model for a possible horizontal gene transfer of the Pyl trait to archaea and bacteria is shown. Ancient (probably extinct) Pyl users are indicated by a light blue circle, and the last universal common ancestor (LUCA) of eukaryotes, bacteria and archaea is shown in dark blue. Dotted lines show a possible Pyl trait transfer.