4. There are sporadic alterations of the universal code

7.4 There are sporadic alterations of the universal code

The universality of the genetic code is striking, but some exceptions exist. They tend to affect the codons involved in initiation or termination and result from the production (or absence) of tRNAs representing certain codons. Almost all of the changes found in principal (bacterial or nuclear) genomes affect termination codons:

• In the prokaryote Mycoplasma capricolum, UGA is not used for termination, but instead codes for tryptophan. In fact, it is the predominant Trp codon, and UGG is used only rarely. Two Trp-tRNA species exist, with the anticodons UCA^← (reads UGA and UGG) and CCA^← (reads only UGG).
  
• Some ciliates (unicellular protozoa) read UAA and UAG as glutamine instead of termination signals. Tetrahymena thermophila, one of the ciliates, contains three tRNA^Glu species. One recognizes the usual codons CAA and CAG for glutamine, one recognizes both UAA and UAG (in accordance with the wobble hypothesis), and the last recognizes only UAG. We assume that a further change is that the release factor eRF has a restricted specificity, compared with that of other eukaryotes.
  
• In another ciliate (Euplotes octacarinatus), UGA codes for cysteine. Only UAA is used as a termination codon, and UAG is not found. The change in meaning of UGA might be accomplished by a modification in the anticodon of tRNA^Cys to allow it to read UGA with the usual codons UGU and UGC.
  
• The only substitution in coding for amino acids occurs in a yeast (Candida), where CUG means serine instead of leucine (and UAG is used as a sense codon).

All of these changes are sporadic, which is to say that they appear to have occurred independently in specific lines of evolution. They may be concentrated on termination codons, because these changes do not involve substitution of one amino acid for another. So the divergent uses of the termination codons could represent their "capture" for normal coding purposes. If some termination codons were used only rarely, they could be recruited to coding purposes by changes that allowed tRNAs to recognize them.

Figure 7.9 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 earlyAUA=Met change was reversed in echinoderms.

Exceptions to the universal genetic code also occur in the mitochondria from several species. Figure 7.9 constructs a phylogeny for the changes. It 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 code for tryptophan, which is common to all (non-plant) mitochondria (for review see 41).

Some of these changes make the code simpler, by replacing two codons that had different meanings with a pair that has a single meaning. Pairs treated like 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 in the mitochondrial code? Because the mitochondrion synthesizes only a small number of proteins (~10), the problem of disruption by changes in meaning is much less severe. Probably the codons that are altered were not used extensively in locations where amino acid substitutions would have been deleterious. The variety of changes found in mitochondria of different species suggests that they have evolved separately, and not by common descent from an ancestral mitochondrial code.

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 codon family and 1 tRNA is needed per codon pair or single codon). But an unusual situation exists in (at least) mammalian mitochondria in which there are only 22 different tRNAs. How does this limited set of tRNAs accommodate all the codons?

The critical feature lies in a simplification of codon-anticodon pairing, in which one tRNA recognizes all four members of a codon family. This reduces to 23 the minimum number of tRNAs required to respond to all usual codons. The use of AG^A_G for termination reduces the requirement by one further tRNA, to 22.

In all eight codon families, the sequence of the tRNA contains an unmodified U at the first position of the anticodon. The remaining codons are grouped into pairs in which all the codons ending in pyrimidines are read by G in the anticodon, and all the codons ending in purines are read by a modified U in the anticodon, as predicted by the wobble hypothesis. The complication of the single UGG codon is avoided by the change in the code to read UGA with UGG as tryptophan; and in mammals, AUA ceases to represent isoleucine and instead is read with AUG as methionine. This allows all the nonfamily codons to be read as 14 pairs.

The 22 identified tRNA genes therefore code for 14 tRNAs representing pairs, and 8 tRNAs representing families. This leaves the two usual termination codons UAG and UAA unrecognized by tRNA, together with the codon pair AG^A_G. Similar rules are followed in the mitochondria of fungi (for review see 33).

As well as these general changes in the code, specific changes in reading occur in individual genes. The specificity of such changes implies that the reading of the particular codon must be influenced by the surrounding bases (also see later).

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 codes for 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 39).

Reviews
33:	Fox, T. D. (1987). Natural variation in the genetic code. Ann. Rev. Genet. 21, 67-91.
39:	Bock, A. (1991). Selenoprotein synthesis: an expansion of the genetic code. Trends Biochem. Sci. 16, 463-467.
41:	Osawa, S. et al. (1992). Recent evidence for evolution of the genetic code. Microbiol. Rev. 56, 229-264.