Vertebrate mitochondrial code

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

Stop codons

AGA and AGG

AGA and AGG are not found to map to any amino acid in vertebrate mitogenomes, and in some cases appear to act as stop codons (as far as comparison of the mRNA against the produced peptide goes). Because these codons do code for amino acids in other animal mitogenomes, this seems to be a shared feature of vertebrates, occurring early in their evolution.

However, at least in humans it has now been shown that AGA and AGG sequences are not recognized as termination codons by MTRF1 or MTRF1L (the release factors). Instead, the mitoribosome ends up stalling because there is no tRNA for reading them, and a -1 frameshift eventually occurs to move the ribosome back to a regular UAG stop codon. In the two human mRNAs with these pseudo-stop codons (CO1 and ND6), a 3' UTR with some secondary structure helps make sure this process happen by deterring translational readthrough. Presumably this is also the process in vertebrates with similar pseudo-stop codons.

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.

Translation table

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

Differences from the standard code

DNA codonsRNA codonsThis code (2)Standard code (1)
AGAAGASTOP = Ter (*)Arg (R)
AGGAGGSTOP = Ter (*)Arg (R)
ATAAUAMet (M)Ile (I)
TGAUGATrp (W)STOP = Ter (*)

Alternative initiation codons

See also

References

  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)
  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.
  3. ↑ Temperley, Richard J.; Wydro, Mateusz; Lightowlers, Robert N.; Chrzanowska-Lightowlers, Zofia M. (2010). "Human mitochondrial mRNAs--like members of all families, similar but different". Biochimica Et Biophysica Acta. 1797 (6–7): 1081–1085. doi:10.1016/j.bbabio.2010.02.036. PMC 3003153. PMID 20211597.
  4. ↑ 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.
  5. ↑ 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)
  6. ↑ 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.
  7. ↑ 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.
  8. ↑ 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.
  9. ↑ 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.
  10. ↑ The Genetic Codes