The Universal Code Has Experienced Sporadic Alterations

KEY CONCEPTS
- Changes in the universal genetic code have occurred in some species.
- These changes are more common in mitochondrial genomes, where a phylogenetic tree can be constructed for the changes.
- In nuclear genomes, the changes usually affect only termination codons.
The universality of the genetic code is striking, but some exceptions exist. They tend to affect the codons involved in initiation or termination. The changes found in principal (bacterial or eukaryotic nuclear) genomes are summarized in FIGURE 1.

FIGURE 1. Changes in the genetic code in bacterial or eukaryotic nuclear genomes usually assign amino acids to stop codons or change a codon so that it no longer specifies an amino acid. A change in meaning from one amino acid to another is unusual.
Almost all of the changes in bacterial or eukaryotic nuclear genomes that allow a codon to represent an amino acid affect termination codons:
- In the prokaryote Mycoplasma capricolum, UGA is not used for termination but instead encodes tryptophan (Trp). In fact, it is the predominant Trp codon, and UGG is used only rarely. Two tRNA^Trp types exist, which have the anticodons UCA← (which reads UGA and UGG) and CCA← (which reads only UGG).
- Some ciliates (unicellular protozoa) read UAA and UAG as glutamine instead of as termination signals. Tetrahymena thermophila, a ciliate, contains three tRNA_^Gln types: One tRNA_^Gln with a UUG anticodon recognizes the usual codons CAA and CAG for glutamine, a second type with the anticodon UUA recognizes both UAA and UAG (in accordance with the wobble hypothesis), and a third type with the anticodon CUA recognizes only UAG. Restriction of the specificity of the release factor eRF so that it recognizes only the UGA stop codon is also necessary to prevent premature termination at the newly reassigned glutamine codons.
- In the ciliate Euplotes octacarinatus, the UGA stop codon is reassigned to cysteine. Only UAA is used as a termination codon, and UAG is not found. The change in meaning of UGA might be accomplished by modifying the anticodon of tRNA with I34 so that it is able to read UGA together with the usual codons UGU and UGC. UGA has dual meaning in E. crassus .
- In a yeast (Candida), CUG is reassigned to serine instead of leucine. This is a rare example of reassignment from one sense codon to another.
In general, acquisition of a coding function by a termination codon requires two types of change: A tRNA must be mutated so as to recognize the codon, and the class I release factor must be altered so that it does not terminate at this codon. The other common type of change is loss of the tRNA that recognizes a particular codon so that that codon no longer specifies any amino acid.
All of these changes are sporadic, meaning that they appear to have occurred independently in specific evolutionary lineages. They may be concentrated in termination codons because at these positions there is no substitution of one amino acid for another. Once the genetic code was established, early in evolution, any general change in the meaning of a codon would cause a substitution in all the proteins that contain that amino acid. It seems likely that the change would be deleterious in at least some of these proteins, with the result that it would be strongly selected against. The divergent uses of the termination codons could represent their “capture” for normal coding purposes. If some termination codons were used only rarely, their recruitment to coding purposes, by way of changes in tRNAs that permit reassignment, would have been more likely.
Exceptions to the universal genetic code also occur in the mitochondria of several species. FIGURE 2 shows a phylogeny for the changes. The ability to construct such a phylogeny suggests that there was a universal code that was changed at various points in mitochondrial evolution. The earliest change was the employment of UGA to encode tryptophan, which is common to mitochondria in all eukaryotes except plants.

FIGURE 2.Changes in the genetic code in mitochondria can be traced in phylogeny. The minimum number of independent changes is generated by supposing that the AUA = Met and the AAA = Asn changes each occurred independently twice and that the early AUA = Met change was reversed in echinoderms.
Some of the mitochondrial changes make the code simpler by replacing two codons that had different meanings with a pair that has a single meaning. Examples of this include UGG and UGA (both Trp instead of one Trp and one termination) and AUG and AUA (both Met instead of one Met and the other Ile).

Why have changes been able to evolve more readily in the mitochondrial code as compared to that of the nucleus? The mitochondrion synthesizes only a small number of proteins (about 10), and, as a result, the problem of disruption by changes in meaning is much less severe. It is likely that the codons that are altered were not used extensively in locations where amino acid
substitutions would have been deleterious.
According to the wobble hypothesis, a minimum of 31 tRNAs (excluding the initiator) are required to recognize all 61 codons (at least 2 tRNAs are required for each 4-codon family and 1 tRNA is needed per codon pair or single codon). However, the streamlined mammalian mitochondrial genome encodes only 22 tRNAs. Other than a few redundant tRNAs that are also encoded in the mitochondrial genome, tRNAs encoded in the nuclear genome are not imported into the mitochondrion in mammals, so it can be inferred there must be some modification to the wobble rules for translation on the mitochondrial ribosome. Interestingly, in
mitochondria an unmodified uridine at the first position of the anticodon is able to pair with all four bases at the third codon position. Such an unmodified uridine exists for the tRNAs representing all eight four-codon families: Pro, Thr, Ala, Ser, Leu, Val, Gly, and Arg. This reduces the total number of tRNAs required in mitochondria by eight. The conversion of AGA and AGG to stop codons in mammalian mitochondria eliminates the need for one additional tRNA, bringing the total required number of tRNAs to just 22. The conversion of AUA to methionine further eliminates the Ile need for inosine modification at position 34 of tRNA .
The different wobble rules for mitochondrial and nuclear translation very likely arise from differences in the detailed structures of the respective ribosomes that translate the two genomes. In cytoplasmic ribosomes, modifications to U34 are used to expand the decoding capacities of certain tRNAs . On mitochondrial ribosomes, modifications to U34 are instead used to restrict pairing to codons containing A or G at the third position, according to the usual wobble rules. Modifications to U34 are indeed found in mitochondrial tRNAs representing amino acids for two-codon sets, thus avoiding the misreading that would otherwise occur.