The term nonsense codons is usually used for the stop codons of the genetic code that do not code for any amino acid and are used to terminate translation during protein biosynthesis . Unassigned codons are codons corresponding to neither amino acids nor stop codons and do not exist in the open reading frames (ORF) of genes coding for proteins. Such codons should be called the real nonsense codons because they are recognized by neither tRNA nor release factors (RF), the proteins that function to terminate translation (see Stop Codons). Such unassigned codons have been recognized only with determination of the sequences of the entire genomes of mitochondria and of some organisms with small genomes. To be an unassigned codon, the tRNA or RF corresponding to this codon probably disappeared from the translation system (1). The unassigned codons determined thus far (2-6) are shown in Table 1. Recently, it has been shown that AAA is unassigned in a hemichordate (7). AAA is assigned to lysine in most metazoans and to asparagine in echinoderms. The situation in hemichordates may be an intermediate en route to the related echinoderms (7).
Table 1. Unassigned Codons*a
|
System |
Probable Unassigned Codon |
Cause |
|
Mycoplasma capricolum |
CGG(Arg)*b |
AT-pressure; lack of tRNAArgCCG |
|
Micrococcus luteus |
AGA(Arg) |
GC-pressure; lack of tRNAArg*UCU |
|
AUA(Ile) |
GC-pressure; lack of tRNAIleLAU |
|
|
Torulopsis glabrata |
||
|
mitochondriaCGN (Arg) |
AT-pressure; lack of tRNAArgCCG |
|
Prototheca wickerhamii |
||
|
(A green alga mitochondria) |
CGN(Arg) |
AT-pressure; lack of tRNAArgCCG |
|
UGA(Stop) |
AT-pressure;? Lack of |
|
|
or UAG(Stop) |
RF-2 |
AT-pressure;? Lack of RF-1 |
|
Drosophila*cand |
AGG(Ser) |
?AT-pressure; lack of tRNASer*GCU (2) |
|
Mosquito* d mitochondria |
(2) |
The appearance of unassigned codons may be caused by direct mutation pressure (as a result of changes in the overall AT and GC content of the genome DNA), change of release factor, or genome economization (Table 1). It is regarded as an intermediate step in codon reassignment in producing genetic code variations (1, 2). The presence of unassigned codons is important evidence for the codon capture theory (1, 2) (see "Candida code and codon reassignment theories" section in Genetic Code).
