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The bacterial, archaeal and plant plastid code (translation table 11) is the DNA code used by bacteria, archaea, prokaryotic viruses and chloroplast proteins. It is essentially the same as the standard code, however there are some variations in alternative start codons.

The code

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.

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.

See also

• List of genetic codes

References

This article incorporates text from the United States National Library of Medicine, which is in the public domain.

1. Elzanowski A, Ostell J (7 January 2019). "The Genetic Codes". National Center for Biotechnology Information. Archived from the original on 5 October 2020. Retrieved 21 February 2019.
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15. Polard, P; Prère, MF; Chandler, M; Fayet, O (5 December 1991). "Programmed translational frameshifting and initiation at an AUU codon in gene expression of bacterial insertion sequence IS911". Journal of Molecular Biology. 222 (3): 465–77. doi:10.1016/0022-2836(91)90490-w. PMID 1660923.
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• Molecular genetics
• Gene expression
• Protein biosynthesis