Vertebrate mitochondrial code

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

Evolution[edit]

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[edit]

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[edit]

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[edit]


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[edit]

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

References[edit]

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]

[A]

[7]

[8]

[9]