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  • 21 Aug, 2019

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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. 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 second codon position best determines amino acid hydrophobicity. Color-coding: hydrophobicity from microenvironment in folded proteins

The classical table/wheel of the standard genetic code is arbitrarily organized based on codon position 1. Saier, following observations from, 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

Amino-acid biochemical properties Nonpolar (np) Polar (p) Basic (b) Acidic (a) Termination: stop codon * Initiation: possible start codon ⇒
Standard genetic code
1st
base 		2nd base 3rd
base
U C A G
U UUU (Phe/F) Phenylalanine (np) UCU (Ser/S) Serine (p) UAU (Tyr/Y) Tyrosine (p) UGU (Cys/C) Cysteine (p) U
UUC UCC UAC UGC C
UUA (Leu/L) Leucine (np) UCA UAA Stop (Ochre) * UGA Stop (Opal) * A
UUG ⇒ UCG UAG Stop (Amber) * UGG (Trp/W) Tryptophan (np) G
C CUU CCU (Pro/P) Proline (np) CAU (His/H) Histidine (b) CGU (Arg/R) Arginine (b) U
CUC CCC CAC CGC C
CUA CCA CAA (Gln/Q) Glutamine (p) CGA A
CUG CCG CAG CGG G
A AUU (Ile/I) Isoleucine (np) ACU (Thr/T) Threonine (p) AAU (Asn/N) Asparagine (p) AGU (Ser/S) Serine (p) U
AUC ACC AAC AGC C
AUA ACA AAA (Lys/K) Lysine (b) AGA (Arg/R) Arginine (b) A
AUG ⇒ (Met/M) Methionine (np) ACG AAG AGG G
G GUU (Val/V) Valine (np) GCU (Ala/A) Alanine (np) GAU (Asp/D) Aspartic acid (a) GGU (Gly/G) Glycine (np) U
GUC GCC GAC GGC C
GUA GCA GAA (Glu/E) Glutamic acid (a) GGA A
GUG ⇒ GCG GAG GGG G

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

Inverse RNA codon table

Inverse table for the standard genetic code (compressed using IUPAC notation)
Amino acid RNA codons Compressed Amino acid RNA codons Compressed
Ala, A GCU, GCC, GCA, GCG GCN Ile, I AUU, AUC, AUA AUH
Arg, R CGU, CGC, CGA, CGG; AGA, AGG CGN, AGR; or
CGY, MGR 		Leu, L CUU, CUC, CUA, CUG; UUA, UUG CUN, UUR; or
CUY, YUR
Asn, N AAU, AAC AAY Lys, K AAA, AAG AAR
Asp, D GAU, GAC GAY Met, M AUG
Asn or Asp, B AAU, AAC; GAU, GAC RAY Phe, F UUU, UUC UUY
Cys, C UGU, UGC UGY Pro, P CCU, CCC, CCA, CCG CCN
Gln, Q CAA, CAG CAR Ser, S UCU, UCC, UCA, UCG; AGU, AGC UCN, AGY
Glu, E GAA, GAG GAR Thr, T ACU, ACC, ACA, ACG ACN
Gln or Glu, Z CAA, CAG; GAA, GAG SAR Trp, W UGG
Gly, G GGU, GGC, GGA, GGG GGN Tyr, Y UAU, UAC UAY
His, H CAU, CAC CAY Val, V GUU, GUC, GUA, GUG GUN
START AUG, CUG, UUG HUG STOP UAA, UGA, UAG URA, UAG; or
UGA, UAR

Standard DNA codon table

Amino-acid biochemical properties Nonpolar (np) Polar (p) Basic (b) Acidic (a) Termination: stop codon * Initiation: possible start codon ⇒
Standard genetic code
1st
base 		2nd base 3rd
base
T C A G
T TTT (Phe/F) Phenylalanine (np) TCT (Ser/S) Serine (p) TAT (Tyr/Y) Tyrosine (p) TGT (Cys/C) Cysteine (p) T
TTC TCC TAC TGC C
TTA (Leu/L) Leucine (np) TCA TAA Stop (Ochre) * TGA Stop (Opal) * A
TTG ⇒ TCG TAG Stop (Amber) * TGG (Trp/W) Tryptophan (np) G
C CTT CCT (Pro/P) Proline (np) CAT (His/H) Histidine (b) CGT (Arg/R) Arginine (b) T
CTC CCC CAC CGC C
CTA CCA CAA (Gln/Q) Glutamine (p) CGA A
CTG CCG CAG CGG G
A ATT (Ile/I) Isoleucine (np) ACT (Thr/T) Threonine (p) AAT (Asn/N) Asparagine (p) AGT (Ser/S) Serine (p) T
ATC ACC AAC AGC C
ATA ACA AAA (Lys/K) Lysine (b) AGA (Arg/R) Arginine (b) A
ATG ⇒ (Met/M) Methionine (np) ACG AAG AGG G
G GTT (Val/V) Valine (np) GCT (Ala/A) Alanine (np) GAT (Asp/D) Aspartic acid (a) GGT (Gly/G) Glycine (np) T
GTC GCC GAC GGC C
GTA GCA GAA (Glu/E) Glutamic acid (a) GGA A
GTG ⇒ GCG GAG GGG G

Inverse DNA codon table

Inverse table for the standard genetic code (compressed using IUPAC notation)
Amino acid DNA codons Compressed Amino acid DNA codons Compressed
Ala, A GCT, GCC, GCA, GCG GCN Ile, I ATT, ATC, ATA ATH
Arg, R CGT, CGC, CGA, CGG; AGA, AGG CGN, AGR; or
CGY, MGR 		Leu, L CTT, CTC, CTA, CTG; TTA, TTG CTN, TTR; or
CTY, YTR
Asn, N AAT, AAC AAY Lys, K AAA, AAG AAR
Asp, D GAT, GAC GAY Met, M ATG
Asn or Asp, B AAT, AAC; GAT, GAC RAY Phe, F TTT, TTC TTY
Cys, C TGT, TGC TGY Pro, P CCT, CCC, CCA, CCG CCN
Gln, Q CAA, CAG CAR Ser, S TCT, TCC, TCA, TCG; AGT, AGC TCN, AGY
Glu, E GAA, GAG GAR Thr, T ACT, ACC, ACA, ACG ACN
Gln or Glu, Z CAA, CAG; GAA, GAG SAR Trp, W TGG
Gly, G GGT, GGC, GGA, GGG GGN Tyr, Y TAT, TAC TAY
His, H CAT, CAC CAY Val, V GTT, GTC, GTA, GTG GTN
START ATG, TTG, GTG, CTG NTG STOP TAA, TGA, TAG TRA, TAR

Alternative codons in other translation tables

Further information: List of genetic codes

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.

Amino-acid biochemical properties Nonpolar (np) Polar (p) Basic (b) Acidic (a) Termination: stop codon *
Comparison between codon translations with alternative and standard genetic codes
Code Translation
table 		DNA codon involved RNA codon involved Translation
with this code 		Standard translation Notes
Standard 1 Includes translation table 8 (plant chloroplasts).
Vertebrate mitochondrial 2 AGA AGA Stop * Arg (R) (b)
AGG AGG Stop * Arg (R) (b)
ATA AUA Met (M) (np) Ile (I) (np)
TGA UGA Trp (W) (np) Stop *
Yeast mitochondrial 3 ATA AUA Met (M) (np) Ile (I) (np)
CTT CUU Thr (T) (p) Leu (L) (np)
CTC CUC Thr (T) (p) Leu (L) (np)
CTA CUA Thr (T) (p) Leu (L) (np)
CTG CUG Thr (T) (p) Leu (L) (np)
TGA UGA Trp (W) (np) Stop *
CGA CGA absent Arg (R) (b)
CGC CGC absent Arg (R) (b)
Mold, protozoan, and coelenterate mitochondrial + Mycoplasma / Spiroplasma 4 TGA UGA Trp (W) (np) Stop * Includes the translation table 7 (kinetoplasts).
Invertebrate mitochondrial 5 AGA AGA Ser (S) (p) Arg (R) (b)
AGG AGG Ser (S) (p) Arg (R) (b)
ATA AUA Met (M) (np) Ile (I) (np)
TGA UGA Trp (W) (np) Stop *
Ciliate, dasycladacean and Hexamita nuclear 6 TAA UAA Gln (Q) (p) Stop *
TAG UAG Gln (Q) (p) Stop *
Echinoderm and flatworm mitochondrial 9 AAA AAA Asn (N) (p) Lys (K) (b)
AGA AGA Ser (S) (p) Arg (R) (b)
AGG AGG Ser (S) (p) Arg (R) (b)
TGA UGA Trp (W) (np) Stop *
Euplotid nuclear 10 TGA UGA Cys (C) (p) Stop *
Bacterial, archaeal and plant plastid 11 See translation table 1.
Alternative yeast nuclear 12 CTG CUG Ser (S) (p) Leu (L) (np)
Ascidian mitochondrial 13 AGA AGA Gly (G) (np) Arg (R) (b)
AGG AGG Gly (G) (np) Arg (R) (b)
ATA AUA Met (M) (np) Ile (I) (np)
TGA UGA Trp (W) (np) Stop *
Alternative flatworm mitochondrial 14 AAA AAA Asn (N) (p) Lys (K) (b)
AGA AGA Ser (S) (p) Arg (R) (b)
AGG AGG Ser (S) (p) Arg (R) (b)
TAA UAA Tyr (Y) (p) Stop *
TGA UGA Trp (W) (np) Stop *
Blepharisma nuclear 15 TAG UAG Gln (Q) (p) Stop * As of Nov. 18, 2016: absent from the NCBI update. Similar to translation table 6.
Chlorophycean mitochondrial 16 TAG UAG Leu (L) (np) Stop *
Trematode mitochondrial 21 TGA UGA Trp (W) (np) Stop *
ATA AUA Met (M) (np) Ile (I) (np)
AGA AGA Ser (S) Arg (R) (b)
AGG AGG Ser (S) (p) Arg (R) (b)
AAA AAA Asn (N) (p) Lys (K) (b)
Scenedesmus obliquus mitochondrial 22 TCA UCA Stop * Ser (S) (p)
TAG UAG Leu (L) (np) Stop *
Thraustochytrium mitochondrial 23 TTA UUA Stop * Leu (L) (np) Similar to translation table 11.
Pterobranchia mitochondrial 24 AGA AGA Ser (S) (p) Arg (R) (b)
AGG AGG Lys (K) (b) Arg (R) (b)
TGA UGA Trp (W) (np) Stop *
Candidate division SR1 and Gracilibacteria 25 TGA UGA Gly (G) (np) Stop *
Pachysolen tannophilus nuclear 26 CTG CUG Ala (A) (np) Leu (L) (np)
Karyorelict nuclear 27 TAA UAA Gln (Q) (p) Stop *
TAG UAG Gln (Q) (p) Stop *
TG UGA Stop * or Trp (W) (np) Stop *
Condylostoma nuclear 28 TAA UAA Stop * or Gln (Q) (p) Stop *
TAG UAG Stop * or Gln (Q) (p) Stop *
TGA UGA Stop * or Trp (W) (np) Stop *
Mesodinium nuclear 29 TAA UAA Tyr (Y) (p) Stop *
TAG UAG Tyr (Y) (p) Stop *
Peritrich nuclear 30 TA UAA Glu (E) (a) Stop *
TAG UAG Glu (E) (a) Stop *
Blastocrithidia nuclear 31 TAA UAA Stop * or Glu (E) (a) Stop *
TAG UAG Stop * or Glu (E) (a) Stop *
TGA UGA Trp (W) (np) Stop *
Cephalodiscidae mitochondrial code 33 AGA AGA Ser (S) (p) Arg (R) (b) Similar to translation table 24.
AGG AGG Lys (K) (b) Arg (R) (b)
TAA UAA Tyr (Y) (p) Stop *
TGA UGA Trp (W) (np) Stop *
Enterosoma 34 AGG AGG Met (M) (np) Arg (R) (b)
Peptacetobacter 35 CGG CGG Gln (Q) (p) Arg (R) (b)
Anaerococcus and Onthovivens 36 CGG CGG Trp (W) (np) Arg (R) (b)
Absconditabacteraceae 37 CGA CGA Trp (W) (np) Arg (R) (b)
CGG CGG Trp (W) (np) Arg (R) (b)
TGA UGA Gly (G) (np) Stop *

See also

Notes

  1. ^ Each stop codon has a specific name: UAG is amber, UGA is opal or umber, and UAA is ochre. In DNA, these stop codons are TAG, TGA, and TAA, respectively.
  2. ^ The historical basis for designating the stop codons as amber, ochre and opal is described in the autobiography of Sydney Brenner and in a historical article by Bob Edgar.
  3. ^ The major difference between DNA and RNA is that thymine (T) is only found in the former. In RNA, it is replaced with uracil (U). This is the only difference between the standard RNA codon table and the standard DNA codon table.
  4. ^ Euplotes octacarinatus is an exception.

References

  1. ^ "Amino Acid Translation Table". Oregon State University. Archived from the original on 29 May 2020. Retrieved 2 December 2020.
  2. ^ Bartee, Lisa; Brook, Jack. MHCC Biology 112: Biology for Health Professions. Open Oregon. p. 42. Archived from the original on 6 December 2020. Retrieved 6 December 2020.
  3. ^ 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.
  4. ^ "RNA Functions". Scitable. Nature Education. Archived from the original on 18 October 2008. Retrieved 5 January 2021.
  5. ^ "The Genetic Codes". National Center for Biotechnology Information. Archived from the original on 13 May 2011. Retrieved 2 December 2020.
  6. ^ "Codon". National Human Genome Research Institute. Archived from the original on 22 October 2020. Retrieved 10 October 2020.
  7. ^ Maloy S. (29 November 2003). "How nonsense mutations got their names". Microbial Genetics Course. San Diego State University. Archived from the original on 23 September 2020. Retrieved 10 October 2020.
  8. ^ Hinnebusch AG (2011). "Molecular Mechanism of Scanning and Start Codon Selection in Eukaryotes". Microbiology and Molecular Biology Reviews. 75 (3): 434–467. doi:10.1128/MMBR.00008-11. PMC 3165540. PMID 21885680.
  9. ^ Touriol C, Bornes S, Bonnal S, Audigier S, Prats H, Prats AC, Vagner S (2003). "Generation of protein isoform diversity by alternative initiation of translation at non-AUG codons". Biology of the Cell. 95 (3–4): 169–78. doi:10.1016/S0248-4900(03)00033-9. PMID 12867081.
  10. ^ Bandyopadhyay, Debashree; Mehler, Ernest L. (August 2008). "Quantitative expression of protein heterogeneity: Response of amino acid side chains to their local environment". Proteins. 72 (2): 646–59. doi:10.1002/prot.21958. PMID 18247345.
  11. ^ Saier, Milton H. Jr. (10 July 2019). "Understanding the Genetic Code". J Bacteriol. 201 (15): e00091-19. doi:10.1128/JB.00091-19. PMC 6620406. PMID 31010904.
  12. ^ Muto, A.; Osawa, S. (January 1987). "The guanine and cytosine content of genomic DNA and bacterial evolution". Proc Natl Acad Sci USA. 84 (1): 166–9. Bibcode:1987PNAS...84..166M. doi:10.1073/pnas.84.1.166. PMC 304163. PMID 3467347.
  13. ^ "The Information in DNA Determines Cellular Function via Translation". Scitable. Nature Education. Archived from the original on 23 September 2017. Retrieved 5 December 2020.
  14. ^ Brenner, Sydney; Wolpert, Lewis (2001). A Life in Science. Biomed Central Limited. pp. 101–104. ISBN 9780954027803.
  15. ^ Edgar B (2004). "The genome of bacteriophage T4: an archeological dig". Genetics. 168 (2): 575–82. doi:10.1093/genetics/168.2.575. PMC 1448817. PMID 15514035. see pages 580–581
  16. ^ IUPAC—IUB Commission on Biochemical Nomenclature. "Abbreviations and Symbols for Nucleic Acids, Polynucleotides and Their Constituents" (PDF). International Union of Pure and Applied Chemistry. Archived (PDF) from the original on 9 July 2021. Retrieved 5 December 2020.
  17. ^ "What does DNA do?". Your Genome. Welcome Genome Campus. Archived from the original on 29 November 2020. Retrieved 12 January 2021.
  18. ^ "Genes". DNA, Genetics, and Evolution. Boston University. Archived from the original on 28 April 2020. Retrieved 10 December 2020.
  19. ^ "Choose a start codon". depts.washington.edu. Retrieved 2024-08-14.
  20. ^ Osawa, A (November 1993). "Evolutionary changes in the genetic code". Comparative Biochemistry and Physiology. 106 (2): 489–94. doi:10.1016/0305-0491(93)90122-l. PMID 8281749. Archived from the original on 2020-12-06. Retrieved 2020-12-05.
  21. ^ Osawa S, Jukes TH, Watanabe K, Muto A (March 1992). "Recent evidence for evolution of the genetic code". Microbiological Reviews. 56 (1): 229–64. doi:10.1128/MR.56.1.229-264.1992. PMC 372862. PMID 1579111.
  22. ^ Shulgina, Yekaterina; Eddy, Sean R. (9 November 2021). "A computational screen for alternative genetic codes in over 250,000 genomes". eLife. 10. doi:10.7554/eLife.71402. PMC 8629427. PMID 34751130.

Further reading

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