Invertebrate mitochondrial code explained

The invertebrate mitochondrial code (translation table 5) is a genetic code used by the mitochondrial genome of invertebrates. Mitochondria contain their own DNA and reproduce independently from their host cell. Variation in translation of the mitochondrial genetic code occurs when DNA codons result in non-standard amino acids has been identified in invertebrates, most notably arthropods.^[1] This variation has been helpful as a tool to improve upon the phylogenetic tree of invertebrates, like flatworms.^[2]

The code

   [[Amino acid|AAs]] = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG

[[Start codon|Starts]] = ---M----------------------------MMMM---------------M------------

 [[DNA#Nucleobase_classification|Base1]] = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG

 Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG

 Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Bases: adenine (A), cytosine (C), guanine (G) and thymine (T) or uracil (U).

Amino acids: Alanine (Ala, A), Arginine (Arg, R), Asparagine (Asn, N), Aspartic acid (Asp, D), Cysteine (Cys, C), Glutamic acid (Glu, E), Glutamine (Gln, Q), Glycine (Gly, G), Histidine (His, H), Isoleucine (Ile, I), Leucine (Leu, L), Lysine (Lys, K), Methionine (Met, M), Phenylalanine (Phe, F), Proline (Pro, P), Serine (Ser, S), Threonine (Thr, T), Tryptophan (Trp, W), Tyrosine (Tyr, Y), Valine (Val, V).

Differences from the standard code

Note: The codon AGG is absent in Drosophila.^[3]

Alternative initiation codons

• ATA/AUA
• ATT/AUU
• ATC/AUC: Apis^[4]
• GTG/GUG: Polyplacophora^[5]
• TTG/UUG: Ascaris, Caenorhabditis.

Systematic range

• Nematoda: Ascaris, Caenorhabditis ;
• Mollusca: Bivalvia);^[6] Polyplacophora;
• Arthropoda/Crustacea: Artemia;^[7]
• Arthropoda/Insecta: Drosophila [<nowiki />''[[Locusta migratoria]] (migratory locust), Apis mellifera (honeybee)].

Other variations

• Several arthropods translate the codon AGG as lysine instead of serine (as in the Pterobranchia Mitochondrial Code) or arginine (as in the standard genetic code).^{[8] [9]}
• GUG may possibly function as an initiator in Drosophila.^{[10] [11]} AUU is not used as an initiator in Mytilus
• "An exceptional mechanism must operate for initiation of translation of the cytochrome oxidase subunit I mRNA in both D. melanogaster^[12] and D. yakuba,^[13] since its only plausible initiation codon, AUA, is out of frame with the rest of the gene. Initiation appears to require the "reading" of an AUAA quadruplet, which would be equivalent to initiation at AUA followed immediately by a specific ribosomal frameshift. Another possible mechanism ... is that the mRNA is "edited" to bring the AUA initiation into frame."^[14]

See also

• List of genetic codes

References

^[15]

Notes and References

1. Abascal . Federico . Posada . David . Knight . Robin D. . Zardoya . Rafael . 2006-04-25 . Parallel Evolution of the Genetic Code in Arthropod Mitochondrial Genomes . PLOS Biology . en . 4 . 5 . e127 . 10.1371/journal.pbio.0040127 . 1545-7885 . 1440934 . 16620150 . free .
2. Telford . Maximilian J. . Herniou . Elisabeth A. . Russell . Robert B. . Littlewood . D. Timothy J. . 2000-10-10 . Changes in mitochondrial genetic codes as phylogenetic characters: Two examples from the flatworms . Proceedings of the National Academy of Sciences . en . 97 . 21 . 11359–11364 . 10.1073/pnas.97.21.11359 . 0027-8424 . 17205 . 11027335 . free .
3. Sengupta S, Yang X, Higgs PG . The mechanisms of codon reassignments in mitochondrial genetic codes . Journal of Molecular Evolution . 64 . 6 . 662–88 . June 2007 . 17541678 . 1894752 . 10.1007/s00239-006-0284-7 . q-bio/0703066 . 2007JMolE..64..662S .
4. Crozier RH, Crozier YC . The mitochondrial genome of the honeybee Apis mellifera: complete sequence and genome organization . Genetics . 133 . 1 . 97–117 . January 1993 . 10.1093/genetics/133.1.97 . 8417993 . 1205303 .
5. Boore JL, Brown WM . Complete DNA sequence of the mitochondrial genome of the black chiton, Katharina tunicata . Genetics . 138 . 2 . 423–43 . October 1994 . 10.1093/genetics/138.2.423 . 7828825 . 1206160 .
6. Hoffmann RJ, Boore JL, Brown WM . A novel mitochondrial genome organization for the blue mussel, Mytilus edulis . Genetics . 131 . 2 . 397–412 . June 1992 . 10.1093/genetics/131.2.397 . 1386586 . 1205014 .
7. Batuecas B, Garesse R, Calleja M, Valverde JR, Marco R . Genome organization of Artemia mitochondrial DNA . Nucleic Acids Research . 16 . 14A . 6515–29 . July 1988 . 3135541 . 338311 . 10.1093/nar/16.14.6515.
8. Abascal F, Posada D, Knight RD, Zardoya R . Parallel evolution of the genetic code in arthropod mitochondrial genomes . PLOS Biology . 4 . 5 . e127 . May 2006 . 16620150 . 1440934 . 10.1371/journal.pbio.0040127 . free .
9. Robinson . Richard . For Arthropod Mitochondria, Variety in the Genetic Code Is Standard . PLOS Biology . 25 April 2006 . 4 . 5 . e175 . 10.1371/journal.pbio.0040175. 20076581 . 1440929 . free .
10. Clary DO, Wolstenholme DR . The mitochondrial DNA molecular of Drosophila yakuba: nucleotide sequence, gene organization, and genetic code . Journal of Molecular Evolution . 22 . 3 . 252–71 . 1985 . 3001325 . 10.1007/BF02099755. 1985JMolE..22..252C . 12384495 .
11. Gadaleta G, Pepe G, De Candia G, Quagliariello C, Sbisà E, Saccone C . Nucleotide sequence of rat mitochondrial NADH dehydrogenase subunit 1. GTG, a new initiator codon in vertebrate mitochondrial genome . Nucleic Acids Research . 16 . 13 . 6233 . July 1988 . 3399396 . 336868 . 10.1093/nar/16.13.6233.
12. de Bruijn MH . Drosophila melanogaster mitochondrial DNA, a novel organization and genetic code . Nature . 304 . 5923 . 234–41 . 1983 . 6408489 . 10.1038/304234a0. 1983Natur.304..234D . 35948584 .
13. Clary DO, Wolstenholme DR . Nucleotide sequence of a segment of Drosophila mitochondrial DNA that contains the genes for cytochrome c oxidase subunits II and III and ATPase subunit 6 . Nucleic Acids Research . 11 . 12 . 4211–27 . June 1983 . 6306579 . 326036 . 10.1093/nar/11.12.4211.
14. Fox TD . Natural variation in the genetic code . Annual Review of Genetics . 21 . 67–91 . 1987 . 3327473 . 10.1146/annurev.ge.21.120187.000435 .
15. Web site: Andrzej . Elzanowski . Jim . Ostell . Detlef . Leipe . Vladimir . Soussov . vanc . The Genetic Codes. 26 August 2015 . Taxonomy browser . National Center for Biotechnology Information (NCBI), U.S. National Library of Medicine .