Bacterial, archaeal and plant plastid code

The code

^A Possible start codons in NCBI table 1. AUG is most common. The two other start codons listed by table 1 (GUG and UUG) are rare in eukaryotes. Prokaryotes have less strigent start codon requirements; they are described by NCBI table 11.

^{B ^ ^ ^} The historical basis for designating the stop codons as amber, ochre and opal is described in an autobiography by Sydney Brenner and in a historical article by Bob Edgar.

As in the standard code, initiation is most efficient at AUG. In addition, GUG and UUG starts are documented in archaea and bacteria. In Escherichia coli, UUG is estimated to serve as initiator for about 3% of the bacterium's proteins. CUG is known to function as an initiator for one plasmid-encoded protein (RepA) in E. coli. In addition to the NUG initiations, in rare cases bacteria can initiate translation from an AUU codon as e.g. in the case of poly(A) polymerase PcnB and the InfC gene that codes for translation initiation factor IF3. The internal assignments are the same as in the standard code though UGA codes at low efficiency for tryptophan in Bacillus subtilis and, presumably, in Escherichia coli.

The NCBI raw format is as follows, with UUG, CUG, AUU, AUC, AUA, AUG, and GUG marked as possible initiators:

AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG Starts = ---M------**--*----M------------MMMM---------------M------------ Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Initiation at AUC and AUA is not addressed in the NCBI description text, but both are indeed known to occur in E. coli.