- Changes in the reading of specific codons can occur in individual genes.
- The insertion of seleno-Cys-tRNA at certain UGA codons requires several proteins to modify the Cys-tRNA and insert it into the ribosome.
- Pyrrolysine can be inserted at certain UAG codons.
Specific changes in reading the code occur in individual genes. The specificity of such changes implies that the reading of the particular codon must be influenced by the surrounding bases.
A striking example is the incorporation of the modified amino acid seleno-cysteine at certain UGA codons within the genes that code for selenoproteins in both prokaryotes and eukaryotes. Usually these proteins catalyze oxidation-reduction reactions, and contain a single seleno-cysteine residue, which forms part of the active site. The most is known about the use of the UGA codons in three E. coli genes coding for formate dehydrogenase isozymes. The internal UGA codon is read by a seleno-Cys-tRNA. This unusual reaction is determined by the local secondary structure of mRNA, in particular by the presence of a hairpin loop downstream of the UGA.
Mutations in 4 sel genes create a deficiency in selenoprotein synthesis. selC codes for tRNA (with the anticodon ACU) that is charged with serine. selA and selD are required to modify the serine to seleno-cysteine. SelB is an alternative elongation factor. It is a guanine nucleotide-binding protein that acts as a specific translation factor for entry of seleno-Cys-tRNA into the A site; it thus provides (for this single tRNA) a replacement for factor EF-Tu. The sequence of SelB is related to both EF-Tu and IF-2 (for review see Bock, 1991).
Why is seleno-Cys-tRNA inserted only at certain UGA codons? These codons are followed by a stem-loop structure in the mRNA. Figure 7.12 shows that the stem of this structure is recognized by an additional domain in SelB (one that is not present in EF-Tu or IF-2). A similar mechanism interprets some UGA codons in mammalian cells, except that two proteins are required to identify the appropriate UGA codons. One protein (SBP2) binds a stem-loop structure far downstream from the UGA codon, while the counterpart of SelB (called SECIS) binds to SBP2 and simultaneously binds the tRNA to the UGA codon (Fagegaltier et al., 2000).
Another example of the insertion of a special amino acid is the placement of pyrrolysine at a UAG codon. This happens in both an archaea and a bacterium (Srinivasan, James, and Krzycki, 2002; Hao et al., 2002). The mechanism is probably similar to the insertion of seleno-cysteine. An unusual tRNA is charged with lysine, which is presumably then modified. The tRNA has a CUA anticodon, which responds to UAG. There must be other components of the system that restricts its response to the appropriate UAG codons.