DNA and RNA codon tables

A codon table can be used to translate a genetic code into a sequence of amino acids. The standard genetic code is traditionally represented as an RNA codon table, because when proteins are made in a cell by ribosomes, it is messenger RNA (mRNA) that directs protein synthesis. The mRNA sequence is determined by the sequence of genomic DNA. In this context, the standard genetic code is referred to as 'translation table 1' among other tables. It can also be represented in a DNA codon table. The DNA codons in such tables occur on the sense DNA strand and are arranged in a 5′-to-3′ direction. Different tables with alternate codons are used depending on the source of the genetic code, such as from a cell nucleus, mitochondrion, plastid, or hydrogenosome.

There are 64 different codons in the genetic code and the below tables; most specify an amino acid. Three sequences, UAG, UGA, and UAA, known as stop codons, do not code for an amino acid but instead signal the release of the nascent polypeptide from the ribosome. In the standard code, the sequence AUG—read as methionine—can serve as a start codon and, along with sequences such as an initiation factor, initiates translation. In rare instances, start codons in the standard code may also include GUG or UUG; these codons normally represent valine and leucine, respectively, but as start codons they are translated as methionine or formylmethionine.

The classical table/wheel of the standard genetic code is arbitrarily organized based on codon position 1. Saier, following observations from Muto, showed that reorganizing the wheel based instead on codon position 2 (and reordering from UCAG to UCGA) better arranges the codons by the hydrophobicity of their encoded amino acids. This suggests that early ribosomes read the second codon position most carefully, to control hydrophobicity patterns in protein sequences.

The first table—the standard table—can be used to translate nucleotide triplets into the corresponding amino acid or appropriate signal if it is a start or stop codon. The second table, appropriately called the inverse, does the opposite: it can be used to deduce a possible triplet code if the amino acid is known. As multiple codons can code for the same amino acid, the International Union of Pure and Applied Chemistry's (IUPAC) nucleic acid notation is given in some instances.

Translation table 1

Standard RNA codon table

As shown in the above table, NCBI table 1 includes the less-canonical start codons GUG and UUG.

Inverse RNA codon table

Standard DNA codon table

Inverse DNA codon table

Alternative codons in other translation tables

The genetic code was once believed to be universal: a codon would code for the same amino acid regardless of the organism or source. However, it is now agreed that the genetic code evolves, resulting in discrepancies in how a codon is translated depending on the genetic source. For example, in 1981, it was discovered that the use of codons AUA, UGA, AGA and AGG by the coding system in mammalian mitochondria differed from the universal code. Stop codons can also be affected: in ciliated protozoa, the universal stop codons UAA and UAG code for glutamine. Four novel alternative genetic codes (numbered here 34–37) were discovered in bacterial genomes by Shulgina and Eddy, revealing the first sense codon changes in bacteria. The following table displays these alternative codons.

See also

• Bioinformatics
• List of genetic codes

Notes

Further reading

• Chevance FV, Hughes KT (2 May 2017). . Proceedings of the National Academy of Sciences of the United States of America. 114 (18): 4745–4750. Bibcode:. doi:. JSTOR . PMC . PMID .
• Dever TE (29 June 2012). . Science. 336 (6089). American Association for the Advancement of Science: 1645–1646. Bibcode:. doi:. JSTOR . PMID . S2CID . from the original on 8 June 2022.
• Gardner RS, Wahba AJ, Basilio C, Miller RS, Lengyel P, Speyer JF (December 1962). . Proceedings of the National Academy of Sciences of the United States of America. 48 (12): 2087–2094. Bibcode:. doi:. PMC . PMID .
• Nakamoto T (March 2009). "Evolution and the universality of the mechanism of initiation of protein synthesis". Gene. 432 (1–2): 1–6. doi:. PMID .
• Wahba AJ, Gardner RS, Basilio C, Miller RS, Speyer JF, Lengyel P (January 1963). . Proceedings of the National Academy of Sciences of the United States of America. 49 (1): 116–122. Bibcode:. doi:. PMC . PMID .
• Yanofsky C (9 March 2007). . Cell. 128 (5): 815–818. doi:. PMID . S2CID .
• Zaneveld J, Hamady M, Sueoka N, Knight R (28 February 2009). "CodonExplorer: An Interactive Online Database for the Analysis of Codon Usage and Sequence Composition". Bioinformatics for DNA Sequence Analysis. Methods in Molecular Biology. Vol. 537. pp. 207–232. doi:. ISBN 978-1-58829-910-9. PMC . PMID .

External links