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J Nucleic Acids
2011 Jan 01;2011:623095. doi: 10.4061/2011/623095.
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tRNA Modification and Genetic Code Variations in Animal Mitochondria.
Watanabe K
,
Yokobori S
.
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In animal mitochondria, six codons have been known as nonuniversal genetic codes, which vary in the course of animal evolution. They are UGA (termination codon in the universal genetic code changes to Trp codon in all animal mitochondria), AUA (Ile to Met in most metazoan mitochondria), AAA (Lys to Asn in echinoderm and some platyhelminth mitochondria), AGA/AGG (Arg to Ser in most invertebrate, Arg to Gly in tunicate, and Arg to termination in vertebrate mitochondria), and UAA (termination to Tyr in a planaria and a nematode mitochondria, but conclusive evidence is lacking in this case). We have elucidated that the anticodons of tRNAs deciphering these nonuniversal codons (tRNA(Trp) for UGA, tRNA(Met) for AUA, tRNA(Asn) for AAA, and tRNA(Ser) and tRNA(Gly) for AGA/AGG) are all modified; tRNA(Trp) has 5-carboxymethylaminomethyluridine or 5-taurinomethyluridine, tRNA(Met) has 5-formylcytidine or 5-taurinomethyluridine, tRNA(Ser) has 7-methylguanosine and tRNA(Gly) has 5-taurinomethyluridine in their anticodon wobble position, and tRNA(Asn) has pseudouridine in the anticodon second position. This review aims to clarify the structural relationship between these nonuniversal codons and the corresponding tRNA anticodons including modified nucleosides and to speculate on the possible mechanisms for explaining the evolutional changes of these nonuniversal codons in the course of animal evolution.
Figure 1. Universal genetic code (inside the box) and variations in animal mt genetic code (outside). Term: termination codon.
Figure 2. Chemical structures of modified nucleosides located at the anticodon wobble position (cmnm5U, τm5U, f5C, and m7G) and the second position (Ψ) of mt tRNAs.
Figure 3. Possible scheme of base pairing between modified nucleosides at the anticodon wobble position and nucleosides at the codon third position in animal mitochondrial translation systems. These structures are only schematic drawing of base-pairing and do not show precise dimension of each nucleoside.
Figure 4. Schematic drawings showing the possible evolutionary changes of UGA (a), AUA (b), AAA (c), and AGR (d) codons in animal mitochondrial genomes. * In order to exclude too complicated situations, simple formulas were adopted for the process of the possible evolutionary changes of AGR codons in this figure. For details, see Text.
Andachi,
Codon recognition patterns as deduced from sequences of the complete set of transfer RNA species in Mycoplasma capricolum. Resemblance to mitochondria.
1989, Pubmed
Andachi,
Codon recognition patterns as deduced from sequences of the complete set of transfer RNA species in Mycoplasma capricolum. Resemblance to mitochondria.
1989,
Pubmed
Anderson,
Sequence and organization of the human mitochondrial genome.
1981,
Pubmed
Barrell,
A different genetic code in human mitochondria.
1979,
Pubmed
Beagley,
The mitochondrial genome of the sea anemone Metridium senile (Cnidaria): introns, a paucity of tRNA genes, and a near-standard genetic code.
1998,
Pubmed
Bessho,
Planarian mitochondria. II. The unique genetic code as deduced from cytochrome c oxidase subunit I gene sequences.
1992,
Pubmed
,
Echinobase
Canny,
Fast cleavage kinetics of a natural hammerhead ribozyme.
2004,
Pubmed
Chimnaronk,
Dual-mode recognition of noncanonical tRNAs(Ser) by seryl-tRNA synthetase in mammalian mitochondria.
2005,
Pubmed
Crick,
Codon--anticodon pairing: the wobble hypothesis.
1966,
Pubmed
Hanada,
Translation ability of mitochondrial tRNAsSer with unusual secondary structures in an in vitro translation system of bovine mitochondria.
2001,
Pubmed
Himeno,
Unusual genetic codes and a novel gene structure for tRNA(AGYSer) in starfish mitochondrial DNA.
1987,
Pubmed
,
Echinobase
Horie,
Modified nucleosides in the first positions of the anticodons of tRNA(Leu)4 and tRNA(Leu)5 from Escherichia coli.
1999,
Pubmed
Jacob,
A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis.
2009,
Pubmed
Kirino,
Codon-specific translational defect caused by a wobble modification deficiency in mutant tRNA from a human mitochondrial disease.
2004,
Pubmed
Kondow,
An extra tRNAGly(U*CU) found in ascidian mitochondria responsible for decoding non-universal codons AGA/AGG as glycine.
1999,
Pubmed
Kurata,
Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U.G wobble pairing during decoding.
2008,
Pubmed
Lavrov,
Mitochondrial genomes of two demosponges provide insights into an early stage of animal evolution.
2005,
Pubmed
Lee,
Isolation of a rat mitochondrial release factor. Accommodation of the changed genetic code for termination.
1987,
Pubmed
Martin,
5-[[(carboxymethyl)amino]methyl]uridine is found in the anticodon of yeast mitochondrial tRNAs recognizing two-codon families ending in a purine.
1990,
Pubmed
Matsuyama,
A novel wobble rule found in starfish mitochondria. Presence of 7-methylguanosine at the anticodon wobble position expands decoding capability of tRNA.
1998,
Pubmed
,
Echinobase
Mizuno,
Stacking of Crick Wobble pair and Watson-Crick pair: stability rules of G-U pairs at ends of helical stems in tRNAs and the relation to codon-anticodon Wobble interaction.
1978,
Pubmed
Moriya,
A novel modified nucleoside found at the first position of the anticodon of methionine tRNA from bovine liver mitochondria.
1994,
Pubmed
Murphy,
Structure of a purine-purine wobble base pair in the decoding center of the ribosome.
2004,
Pubmed
Osawa,
Codon reassignment (codon capture) in evolution.
1989,
Pubmed
Osawa,
Evolution of the mitochondrial genetic code. I. Origin of AGR serine and stop codons in metazoan mitochondria.
1989,
Pubmed
Sakurai,
Unusual usage of wobble modifications in mitochondrial tRNAs of the nematode Ascaris suum.
2005,
Pubmed
Sakurai,
Modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial tRNAs lacking the entire T-arm.
2005,
Pubmed
Schultz,
Transfer RNA mutation and the malleability of the genetic code.
1994,
Pubmed
Sengupta,
The mechanisms of codon reassignments in mitochondrial genetic codes.
2007,
Pubmed
Shimada,
Dual mode recognition of two isoacceptor tRNAs by mammalian mitochondrial seryl-tRNA synthetase.
2001,
Pubmed
Soleimanpour-Lichaei,
mtRF1a is a human mitochondrial translation release factor decoding the major termination codons UAA and UAG.
2007,
Pubmed
Spencer,
Characterization of the human mitochondrial methionyl-tRNA synthetase.
2004,
Pubmed
Suzuki,
Taurine as a constituent of mitochondrial tRNAs: new insights into the functions of taurine and human mitochondrial diseases.
2002,
Pubmed
Suzuki,
Taurine-containing uridine modifications in tRNA anticodons are required to decipher non-universal genetic codes in ascidian mitochondria.
2011,
Pubmed
Suzuki,
The 'polysemous' codon--a codon with multiple amino acid assignment caused by dual specificity of tRNA identity.
1997,
Pubmed
Suzuki,
Human mitochondrial diseases caused by lack of taurine modification in mitochondrial tRNAs.
2011,
Pubmed
Takai,
Recognition of UUN codons by two leucine tRNA species from Escherichia coli.
1994,
Pubmed
Takai,
Classification of the possible pairs between the first anticodon and the third codon positions based on a simple model assuming two geometries with which the pairing effectively potentiates the decoding complex.
2006,
Pubmed
Takemoto,
Unconventional decoding of the AUA codon as methionine by mitochondrial tRNAMet with the anticodon f5CAU as revealed with a mitochondrial in vitro translation system.
2009,
Pubmed
Telford,
Changes in mitochondrial genetic codes as phylogenetic characters: two examples from the flatworms.
2000,
Pubmed
Tomita,
7-Methylguanosine at the anticodon wobble position of squid mitochondrial tRNA(Ser)GCU: molecular basis for assignment of AGA/AGG codons as serine in invertebrate mitochondria.
1998,
Pubmed
,
Echinobase
Tomita,
Codon reading patterns in Drosophila melanogaster mitochondria based on their tRNA sequences: a unique wobble rule in animal mitochondria.
1999,
Pubmed
Tomita,
5-formylcytidine (f5C) found at the wobble position of the anticodon of squid mitochondrial tRNA(Met)CAU.
1997,
Pubmed
Tomita,
The presence of pseudouridine in the anticodon alters the genetic code: a possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondria.
1999,
Pubmed
,
Echinobase
Watanabe,
Unique features of animal mitochondrial translation systems. The non-universal genetic code, unusual features of the translational apparatus and their relevance to human mitochondrial diseases.
2010,
Pubmed
Watanabe,
Primary and higher order structures of nematode (Ascaris suum) mitochondrial tRNAs lacking either the T or D stem.
1994,
Pubmed
Yamao,
UGA is read as tryptophan in Mycoplasma capricolum.
1985,
Pubmed
Yasukawa,
Wobble modification defect suppresses translational activity of tRNAs with MERRF and MELAS mutations.
2002,
Pubmed
Yasukawa,
Wobble modification defect in tRNA disturbs codon-anticodon interaction in a mitochondrial disease.
2001,
Pubmed
Yokobori,
Complete DNA sequence of the mitochondrial genome of the ascidian Halocynthia roretzi (Chordata, Urochordata).
1999,
Pubmed
Yokobori,
Codons AGA and AGG are read as glycine in ascidian mitochondria.
1993,
Pubmed
Yokogawa,
Characterization and tRNA recognition of mammalian mitochondrial seryl-tRNA synthetase.
2000,
Pubmed
Yokoyama,
Molecular mechanism of codon recognition by tRNA species with modified uridine in the first position of the anticodon.
1985,
Pubmed