Genetic Code of mitochondria

From Mitogenome.com

Mitochondria genome is characteristic because it has its own genetic code, sightly different from the "standard" genetic code. Here are the different mitochondrial tables:

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Contents 1 The Vertebrate Mitochondrial Code (transl_table=2) 1.1 Differences from the Standard Code: 1.2 Alternative Initiation Codon: 1.3 Systematic Range: 1.4 Comment: 2 The Yeast Mitochondrial Code (transl_table=3) 2.1 Differences from the Standard Code: 3 The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code (transl_table=4) 3.1 Differences from the Standard Code: 3.2 Alternative Initiation Codons: 3.3 Systematic Range: 4 The Invertebrate Mitochondrial Code (transl_table=5) 4.1 Comment: 4.2 Differences from the Standard Code: 4.3 Alternative Initiation Codons: 4.4 Systematic Range: 4.5 Comments: 5 The Echinoderm and Flatworm Mitochondrial Code (transl_table=9) 5.1 Differences from the Standard Code: 5.2 Systematic Range: 6 The Ascidian Mitochondrial Code (transl_table=13) 6.1 Differences from the Standard Code: 6.2 Systematic range and Comments: 7 The Alternative Flatworm Mitochondrial Code (transl_table=14) 7.1 Differences from the Standard Code: 7.2 Systematic Range: 7.3 Comments: 8 Chlorophycean Mitochondrial Code (transl_table=16) 8.1 Systematic Range: 9 Trematode Mitochondrial Code (transl_table=21) 9.1 Systematic Range: 9.2 Other Alternative Initiation Codons 10 cenedesmus obliquus mitochondrial Code (transl_table=22) 10.1 Systematic Range: 10.2 Other Alternative Initiation Codons 11 Thraustochytrium Mitochondrial Code (transl_table=23)

The Vertebrate Mitochondrial Code (transl_table=2)

    
    AAs  = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG
  Starts = --------------------------------MMMM---------------M------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Differences from the Standard Code:

        Code 2          Standard
 AGA    Ter  *          Arg  R
 AGG    Ter  *          Arg  R
 AUA    Met  M          Ile  I
 UGA    Trp  W          Ter  *

Alternative Initiation Codon:

Bos: AUA
Homo: AUA, AUU
Mus: AUA, AUU, AUC
Coturnix, Gallus: also GUG (Desjardins and Morais, 1991)

Systematic Range:

Vertebrata

Comment:

The transcripts of several vertebrate mitochondrial genes end in U or UA, which become termination codons (UAA) upon subsequent polyadenylation.

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The Yeast Mitochondrial Code (transl_table=3)

    AAs  = FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG
  Starts = ----------------------------------MM----------------------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Differences from the Standard Code:

        Code 3          Standard
 AUA    Met  M          Ile  I
 CUU    Thr  T          Leu  L
 CUC    Thr  T          Leu  L
 CUA    Thr  T          Leu  L
 CUG    Thr  T          Leu  L
 UGA    Trp  W          Ter  *
 CGA    absent          Arg  R
 CGC    absent          Arg  R

Systematic Range: Saccharomyces cerevisiae, Candida glabrata, Hansenula saturnus, and Kluyveromyces thermotolerans (Clark-Walker and Weiller, 1994)

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The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code (transl_table=4)

    
  AAs  = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = --MM---------------M------------MMMM---------------M------------
Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Differences from the Standard Code:

        Code 4         Standard
 UGA    Trp  W          Ter  *

Alternative Initiation Codons:

Trypanosoma: UUA, UUG, CUG
Leishmania: AUU, AUA
Tertrahymena: AUU, AUA, AUG
Paramecium: AUU, AUA, AUG, AUC, GUG, GUA(?)
(Pritchard et al., 1990)

Systematic Range:

Mollicutes: The code is used in Entomoplasmatales and Mycoplasmatales (Bove et al. 1989). The situation in the Acholeplasmatales is unclear. Based on a study of ribosomal protein genes, it had been concluded that UGA does not code for tryptophan in plant-pathogenic mycoplasma-like organisms (MLO) and the Acholeplasmataceae (Lim and Sears, 1992). In contrast, in a study of codon usage in Phytoplasmas, it was found that 30 out of 78 ORFs analyzed translated better with code 4 (UGA for tryptophan) than with code 11 while the remainder showed no differences between the two codes (Melamed et al. 2003).

Fungi: Emericella nidulans, Neurospora crassa, Podospora anserina, Acremonium (Fox, 1987), Candida parapsilosis (Guelin et al., 1991), Trichophyton rubrum (de Bievre and Dujon, 1992), Dekkera/Brettanomyces, Eeniella (Hoeben et al., 1993), and probably Ascobolus immersus, Aspergillus amstelodami, Claviceps purpurea, and Cochliobolus heterostrophus.

Other Eukaryotes: Gigartinales among the red algae (Boyen et al. 1994), and the protozoa Trypanosoma brucei, Leishmania tarentolae, Paramecium tetraurelia, Tetrahymena pyriformis and probably Plasmodium gallinaceum (Aldritt et al., 1989).

Metazoa: Coelenterata (Ctenophora and Cnidaria)

Comments:

• This code is also used for the kinetoplast DNA (maxicircles, minicircles). Kinetoplasts are modified mitochondria (or their parts).

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The Invertebrate Mitochondrial Code (transl_table=5)

    
    AAs  = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG
  Starts = ---M----------------------------MMMM---------------M------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
  

Comment:

The codon AGG is absent in Drosophila.

Differences from the Standard Code:

        Code 5          Standard
 AGA    Ser  S          Arg  R
 AGG    Ser  S          Arg  R
 AUA    Met  M          Ile  I
 UGA    Trp  W          Ter  *
 

Alternative Initiation Codons:

AUA, AUU
AUC: Apis (Crozier and Crozier, 1993)
GUG: Polyplacophora (Boore and Brown, 1994 GenBank Accession Number: U09810)
UUG: Ascaris, Caenorhabditis

Systematic Range:

Nematoda: Ascaris, Caenorhabditis;
Mollusca: Bivalvia (Hoffmann et al., 1992); Polyplacophora (Boore and Brown, 1994)
Arthropoda/Crustacea: Artemia (Batuecas et al., 1988);
Arthropoda/Insecta: Drosophila [Locusta migratoria (migratory locust), Apis mellifera (honeybee)]

Comments:

• Several arthropods translate the codon AGG as lysine instead of serine (as in the invertebrate mitochondrial genetic code) or arginine (as in the standard genetic code) (Abascal et al., 2006).

• GUG may possibly function as an initiator in Drosophila (Clary and Wolstenholme, 1985; Gadaleta et al., 1988). AUU is not used as an initiator in Mytilus (Hoffmann et al., 1992).

• "An exceptional mechanism must operate for initiation of translation of the cytochrome oxidase subunit I mRNA in both D. melanogaster (de Bruijn, 1983) and D. yakuba (Clary and Wolstenholme 1983), since its only plausible initiation codon, AUA, is out of frame with the rest of the gene. Initiation appears to require the "reading" of 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." (Fox, 1987)

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The Echinoderm and Flatworm Mitochondrial Code (transl_table=9)

    
    AAs  = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
  Starts = -----------------------------------M---------------M------------
  Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
  Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
  Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
  

Differences from the Standard Code:

          Code 9        Standard
AAA      Asn  N        Lys K
AGA      Ser  S        Arg R
AGG      Ser  S        Arg R
UGA      Trp  W        Ter *

Systematic Range:

Asterozoa (starfishes) (Himeno et al., 1987) Echinozoa (sea urchins) (Jacobs et al., 1988; Cantatore et al., 1989) Rhabditophora among the Platyhelminthes (Telford et al. 2000)

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The Ascidian Mitochondrial Code (transl_table=13)

    
  AAs  = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG
Starts = ---M------------------------------MM---------------M------------
Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Differences from the Standard Code:

          Code 13     Standard
AGA      Gly  G        Arg  R
AGG      Gly  G        Arg  R
AUA      Met  M        Ile  I
UGA      Trp  W        Ter  *

Systematic range and Comments:

There is evidence from a phylogenetically diverse sample of tunicates (Urochordata) that AGA and AGG code for glycine. In other organisms, AGA/AGG code for either arginine or serine and in vertebrate mitochondria they code a STOP. Evidence for glycine translation of AGA/AGG has been found in Pyura stolonifera (Durrheim et al. 1993), Halocynthia roretzi (Kondow et al. 1999, Yokobori et al., 1993, Yokobori et al. 1999) and Ciona savignyi (Yokobori et al. 2003). In addition, the Halocynthia roretzi mitochondrial genome encodes an additional tRNA gene with the anticodon U*CU that is thought to enable the use of AGA or AGG codons for glycine and the gene has been shown to be transcribed in vivo (Kondow et al. 1999, Yokobori et al. 1999).

Alternative initiation codons: ATA, GTG and TTG (Yokobori et al. 1999).

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The Alternative Flatworm Mitochondrial Code (transl_table=14)

    
 AAs  = FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Differences from the Standard Code:

          Code 14      Standard
AAA      Asn  N       Lys  K
AGA      Ser  S       Arg  R
AGG      Ser  S       Arg  R
UAA      Tyr  Y       Ter  *
UGA      Trp  W       Ter  *

Systematic Range:

Platyhelminthes (flatworms)

Comments:

• Code 14 differs from code 9 only by translating UAA to Tyr rather than STOP. A recent study [PMID:11027335] has found no evidence that the codon UAA codes for Tyr in the flatworms but other opinions exist. There are very few GenBank records that are translated with code 14 but a test translation shows that retranslating these records with code 9 can cause premature terminations. Therefore, GenBank will maintain code 14 until further information become available.

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Chlorophycean Mitochondrial Code (transl_table=16)

    
  AAs  = FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
 Starts = -----------------------------------M----------------------------
 Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
 Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
 Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
 

Systematic Range:

Chlorophyceae (Hayashi-Ishimaru et al. 1996. UAG is a sense codon in several chlorophycean mitochondria) and the chytridiomycete fungus Spizellomyces punctatus (Laforest et al. 1997. Mitochondrial tRNAs in the lower fungus Spizellomyces punctatus: tRNA editing and UAG 'stop' codons recognized as leucine).

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Trematode Mitochondrial Code (transl_table=21)

    
  AAs  = FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG
Starts = -----------------------------------M---------------M------------
Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Systematic Range:

Trematoda: Ohama, T, S. Osawa, K. Watanabe, T.H. Jukes, 1990. J. Molec Evol. 30
Garey, J.R. and D.R. Wolstenholme, 1989. J. Molec. Evol. 28: 374-387 329-332.

Other Alternative Initiation Codons

• GUG, UUG (and possibly CUG) in the Archaea (Noelling et al., 1995)

• AUA, GUG, UUG, and AUC or AAG may be used (at least in experimental systems) by the yeasts Saccharomyces cerevisiae (Olsen, O. (1987) Carlsberg Res. Comm. 52: 83-90, and references therein).

• ACG initiates translation of certain proteins in the adeno-associated virus type 2 (Becerra et al., 1985), the phage T7 mutant CR17 (Anderson and Buzash-Pollert, 1985), Sendai virus (Gupta and Patwardhan, 1988), and rice chloroplast (Hiratsuka et al., 1989). Also, it is the most effective non-AUG initiation codon in mammalin cells (Koepke and Leggatt, 1991).

• CUG is the initiation codon for one of the two alternative products of the human c-myc gene (Hann et al., 1987).

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cenedesmus obliquus mitochondrial Code (transl_table=22)

    
  AAs  = FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = -----------------------------------M----------------------------
Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

Systematic Range:

Scenedesmus obliquus: Nedelcu A, Lee RW, Lemieux C, Gray MW and Burger G. "The complete mitochondrial DNA sequence of Scenedesmus obliquus reflects an intermediate stage in the evolution of the green algal mitochondrial genome." Genome Research (in press).

Other Alternative Initiation Codons

• GUG, UUG (and possibly CUG) in the Archaea (Noelling et al., 1995)

• AUA, GUG, UUG, and AUC or AAG may be used (at least in experimental systems) by the yeasts Saccharomyces cerevisiae (Olsen, 1987, and references therein).

• ACG initiates translation of certain proteins in the adeno-associated virus type 2 (Becerra et al., 1985), the phage T7 mutant CR17 (Anderson and Buzash-Pollert, 1985), Sendai virus (Gupta and Patwardhan, 1988), and rice chloroplast (Hiratsuka et al., 1989). Also, it is the most effective non-AUG initiation codon in mammalin cells (Koepke and Leggatt, 1991).

• CUG is the initiation codon for one of the two alternative products of the human c-myc gene (Hann et al., 1987).

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Thraustochytrium Mitochondrial Code (transl_table=23)

    
  AAs  = FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = --------------------------------M--M---------------M------------
Base1  = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2  = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3  = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG

This code has been created for the mitochondrial genome of the labyrinthulid Thraustochytrium aureum sequenced by the The Organelle Genome Megasequencing Program (OGMP).

It is the similar to the bacterial code (trans_table 11) but it contains an additional stop codon (TTA) and also has a different set of start codons.

Source:
NCBI. Credits: Andrzej (Anjay) Elzanowski, Jim Ostell, Detlef Leipe, Vladimir Soussov.