Vertebrate mitochondrial code

The vertebrate mitochondrial code (translation table 2) is the genetic code found in the mitochondria of all vertebrata.

Evolution

AGA and AGG were thought to have become mitochondrial stop codons early in vertebrate evolution.^[1] However, at least in humans it has now been shown that AGA and AGG sequences are not recognized as termination codons. A -1 mitoribosome frameshift occurs at the AGA and AGG codons predicted to terminate the CO1 and ND6 open reading frames (ORFs), and consequently both ORFs terminate in the standard UAG codon.^[2]

Incomplete stop codons

Mitochondrial genes in some vertebrates (including humans) have incomplete stop codons ending in U or UA, which become complete termination codons (UAA) upon subsequent polyadenylation.^[3]^[4]^[5]^[6]

Translation table

Amino acids biochemical properties	nonpolar	polar	basic	acidic		Termination: stop codon

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

^A The codon AUG both codes for methionine and serves as an initiation site: the first AUG in an mRNA's coding region is where translation into protein begins.^[7]

Differences from the standard code


DNA codons	RNA codons	This code (2)	Standard code (1)
`AGA`	`AGA`	`STOP = Ter` `(*)`	`Arg` `(R)`
`AGG`	`AGG`	`STOP = Ter` `(*)`	`Arg` `(R)`
`ATA`	`AUA`	`Met` `(M)`	`Ile` `(I)`
`TGA`	`UGA`	`Trp` `(W)`	`STOP = Ter` `(*)`

Alternative initiation codons

Bos: AUA
Homo: AUA, AUU
Mus: AUA, AUU, AUC
Coturnix, Gallus: also GUG^[8]

References

This article contains public domain text from the NCBI page compiled by Andrzej Elzanowski and Jim Ostell.^[9]

^ S. Osawa, T. Ohama, T. H. Jukes and K. Watanabe (September 1989). "Evolution of the mitochondrial genetic code. I. Origin of AGR serine and stop codons in metazoan mitochondria". J Mol Evol. 29 (3): 202–7. Bibcode:1989JMolE..29..202O. doi:10.1007/bf02100203. PMID 2506356. S2CID 21051869.{{cite journal}}: CS1 maint: multiple names: authors list (link)
^ R J Temperley; R Richter; S Dennerlein; R N Lightowlers; Z M Chrzanowska-Lightowlers (January 2010). "Hungry codons promote frameshifting in human mitochondrial ribosomes". Science. 327 (5963): 301. Bibcode:2010Sci...327..301T. doi:10.1126/science.1180674. PMID 20075246. S2CID 206522983.
^ Temperley, R. J.; Wydro, M; Lightowlers, R. N.; Chrzanowska-Lightowlers, Z. M. (2010). "Human mitochondrial mRNAs--like members of all families, similar but different". Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1797 (6–7): 1081–5. doi:10.1016/j.bbabio.2010.02.036. PMC 3003153. PMID 20211597.
^ W. R. Hou, Y. Chen, X. Wu, J. C. Hu, Z. S. Peng, J. Yang, Z. X. Tang, C. Q. Zhou, Y. M. Li, S. K. Yang, Y. J. Du, L. L. Kong, Z. L. Ren, H. Y. Zhang and S. S. Shuai (December 2006). "A complete mitochondrial genome sequence of Asian black bear Sichuan subspecies (Ursus thibetanus mupinensis)". Int J Biol Sci. 3 (2): 85–90. doi:10.7150/ijbs.3.85. PMC 1752227. PMID 17205108.{{cite journal}}: CS1 maint: multiple names: authors list (link)
^ Oh, D. J.; Kim, J. Y.; Lee, J. A.; Yoon, W. J.; Park, S. Y.; Jung, Y. H. (2007). "Complete mitochondrial genome of the rabbitfish Siganus fuscescens (Perciformes, Siganidae)". DNA Sequence. 18 (4): 295–301. doi:10.1080/10425170701248525. PMID 17541835. S2CID 38458668.
^ Ki, J. S.; Hwang, D. S.; Park, T. J.; Han, S. H.; Lee, J. S. (2009). "A comparative analysis of the complete mitochondrial genome of the Eurasian otter Lutra lutra (Carnivora; Mustelidae)". Molecular Biology Reports. 37 (4): 1943–55. doi:10.1007/s11033-009-9641-0. PMID 19757186. S2CID 24233602.
^ Nakamoto T (March 2009). "Evolution and the universality of the mechanism of initiation of protein synthesis". Gene. 432 (1–2): 1–6. doi:10.1016/j.gene.2008.11.001. PMID 19056476.
^ P. Desjardins & R. Morais (February 1991). "Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome". J Mol Evol. 32 (2): 153–161. Bibcode:1991JMolE..32..153D. doi:10.1007/bf02515387. PMID 1706782. S2CID 1974138.
^ The Genetic Codes

[OOJ&W-1] S. Osawa, T. Ohama, T. H. Jukes and K. Watanabe (September 1989). "Evolution of the mitochondrial genetic code. I. Origin of AGR serine and stop codons in metazoan mitochondria". J Mol Evol. 29 (3): 202–7. Bibcode:1989JMolE..29..202O. doi:10.1007/bf02100203. PMID 2506356. S2CID 21051869.{{cite journal}}: CS1 maint: multiple names: authors list (link)

[Temperly-2] R J Temperley; R Richter; S Dennerlein; R N Lightowlers; Z M Chrzanowska-Lightowlers (January 2010). "Hungry codons promote frameshifting in human mitochondrial ribosomes". Science. 327 (5963): 301. Bibcode:2010Sci...327..301T. doi:10.1126/science.1180674. PMID 20075246. S2CID 206522983.

[Temperly2-3] Temperley, R. J.; Wydro, M; Lightowlers, R. N.; Chrzanowska-Lightowlers, Z. M. (2010). "Human mitochondrial mRNAs--like members of all families, similar but different". Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1797 (6–7): 1081–5. doi:10.1016/j.bbabio.2010.02.036. PMC 3003153. PMID 20211597.

[Hou-4] W. R. Hou, Y. Chen, X. Wu, J. C. Hu, Z. S. Peng, J. Yang, Z. X. Tang, C. Q. Zhou, Y. M. Li, S. K. Yang, Y. J. Du, L. L. Kong, Z. L. Ren, H. Y. Zhang and S. S. Shuai (December 2006). "A complete mitochondrial genome sequence of Asian black bear Sichuan subspecies (Ursus thibetanus mupinensis)". Int J Biol Sci. 3 (2): 85–90. doi:10.7150/ijbs.3.85. PMC 1752227. PMID 17205108.{{cite journal}}: CS1 maint: multiple names: authors list (link)

[Oh-5] Oh, D. J.; Kim, J. Y.; Lee, J. A.; Yoon, W. J.; Park, S. Y.; Jung, Y. H. (2007). "Complete mitochondrial genome of the rabbitfish Siganus fuscescens (Perciformes, Siganidae)". DNA Sequence. 18 (4): 295–301. doi:10.1080/10425170701248525. PMID 17541835. S2CID 38458668.

[Ki-6] Ki, J. S.; Hwang, D. S.; Park, T. J.; Han, S. H.; Lee, J. S. (2009). "A comparative analysis of the complete mitochondrial genome of the Eurasian otter Lutra lutra (Carnivora; Mustelidae)". Molecular Biology Reports. 37 (4): 1943–55. doi:10.1007/s11033-009-9641-0. PMID 19757186. S2CID 24233602.

[pmid19056476-7] Nakamoto T (March 2009). "Evolution and the universality of the mechanism of initiation of protein synthesis". Gene. 432 (1–2): 1–6. doi:10.1016/j.gene.2008.11.001. PMID 19056476.

[D&M-8] P. Desjardins & R. Morais (February 1991). "Nucleotide sequence and evolution of coding and noncoding regions of a quail mitochondrial genome". J Mol Evol. 32 (2): 153–161. Bibcode:1991JMolE..32..153D. doi:10.1007/bf02515387. PMID 1706782. S2CID 1974138.

[Elzanowski-9] The Genetic Codes

[1]

[2]

[3]

[4]

[5]

[6]

[7]

[8]

[9]