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An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine.

Su D, Lieberman A, Lang BF, Simonovic M, Söll D, Ling J - Nucleic Acids Res. (2011)

Bottom Line: A loss of the first nucleotide (G(-1)) in tRNA(His) converts it to a substrate for MST1 with a K(m) value (0.7 μM) comparable to that of (0.3 μM), and addition of G(-1) to allows efficient histidylation by histidyl-tRNA synthetase.We also show that MST1 from Candida albicans, a yeast in which CUN codons remain assigned to leucine, could not threonylate , suggesting that MST1 has coevolved with .Our work provides the first clear example of a recent recoding event caused by alloacceptor tRNA gene recruitment.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.

ABSTRACT
The standard genetic code is used by most living organisms, yet deviations have been observed in many genomes, suggesting that the genetic code has been evolving. In certain yeast mitochondria, CUN codons are reassigned from leucine to threonine, which requires an unusual tRNA(Thr) with an enlarged 8-nt anticodon loop ( ). To trace its evolutionary origin we performed a comprehensive phylogenetic analysis which revealed that evolved from yeast mitochondrial tRNA(His). To understand this tRNA identity change, we performed mutational and biochemical experiments. We show that Saccharomyces cerevisiae mitochondrial threonyl-tRNA synthetase (MST1) could attach threonine to both and the regular , but not to the wild-type tRNA(His). A loss of the first nucleotide (G(-1)) in tRNA(His) converts it to a substrate for MST1 with a K(m) value (0.7 μM) comparable to that of (0.3 μM), and addition of G(-1) to allows efficient histidylation by histidyl-tRNA synthetase. We also show that MST1 from Candida albicans, a yeast in which CUN codons remain assigned to leucine, could not threonylate , suggesting that MST1 has coevolved with . Our work provides the first clear example of a recent recoding event caused by alloacceptor tRNA gene recruitment.

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Phylogeny of yeast species based on concatenated mtDNA-encoded protein sequences. The phylogenetic analysis with PhyloBayes and the CAT model is based on 13 mtDNA encoded proteins. All divergence points are supported by posterior probability values of 1.0, except where indicated. The red arrow points to the concomitant loss of all seven nad genes and the start of mitochondrial codon reassignments, including AUA methionine, CUN threonine. Species shown in black possess mitochondrial  (but not ), and in these organisms CUN codons are assigned to Leu. The yeast species marked red, such as K. thermotolerans, have lost mitochondrial  and obtained  that decodes CUN codons as Thr. K. lactis is marked magenta as it has no CUN codons and no corresponding tRNA with a UAG anticodon. A. gossypii (marked blue) contains a tRNA species with a UAG anticodon, yet its identity of this tRNA and the amino acid reading CUN codons in A. gossypii remain obscure (to be discussed by BFL in Organelle Genetics: Evolution of Organelle Genomes and Gene Expression, Springer 2011).
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Figure 3: Phylogeny of yeast species based on concatenated mtDNA-encoded protein sequences. The phylogenetic analysis with PhyloBayes and the CAT model is based on 13 mtDNA encoded proteins. All divergence points are supported by posterior probability values of 1.0, except where indicated. The red arrow points to the concomitant loss of all seven nad genes and the start of mitochondrial codon reassignments, including AUA methionine, CUN threonine. Species shown in black possess mitochondrial (but not ), and in these organisms CUN codons are assigned to Leu. The yeast species marked red, such as K. thermotolerans, have lost mitochondrial and obtained that decodes CUN codons as Thr. K. lactis is marked magenta as it has no CUN codons and no corresponding tRNA with a UAG anticodon. A. gossypii (marked blue) contains a tRNA species with a UAG anticodon, yet its identity of this tRNA and the amino acid reading CUN codons in A. gossypii remain obscure (to be discussed by BFL in Organelle Genetics: Evolution of Organelle Genomes and Gene Expression, Springer 2011).

Mentions: The unsolved question of the yeast mitochondrial CUN codon reassignment is the evolutionary origin of with an 8-nt anticodon loop and a UAG anticodon. To analyze the recruitment, we performed a phylogenetic analysis of all mitochondrial tRNAs of S. cerevisiae and related yeast species using Bayesian inference (Figure 2). Not surprisingly, the 10 organisms with are closely related; yet this cluster is related to tRNAHis (72% sequence identity between the two respective S. cerevisiae tRNAs; Figure 1). In contrast, and are definitively distant in the phylogeny (Figures 2, Supplementary Figure S1) and the respective S. cerevisiae tRNAs share only 52% sequence identity. As the phylogenetic signal in tRNA sequences is limited by the small number of informative sequence sites, and not a reliable marker in species phylogenies because of occasional identity shifts [e.g. (28)], we have built a yeast species tree based on mitochondrion-encoded proteins to permit mapping of evolutionary changes to this tree. The result of this phylogenetic analysis (Figure 3) is consistent with a single origin of the 10 yeast species that have a homolog with an 8-nt anticodon loop, a clade emerging close to the divergence of Kluyveromyces species and subsequent to Pichia canadensis. Together, these results strongly suggest that derived from mitochondrial tRNAHis in an ancestral yeast species.Figure 2.


An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine.

Su D, Lieberman A, Lang BF, Simonovic M, Söll D, Ling J - Nucleic Acids Res. (2011)

Phylogeny of yeast species based on concatenated mtDNA-encoded protein sequences. The phylogenetic analysis with PhyloBayes and the CAT model is based on 13 mtDNA encoded proteins. All divergence points are supported by posterior probability values of 1.0, except where indicated. The red arrow points to the concomitant loss of all seven nad genes and the start of mitochondrial codon reassignments, including AUA methionine, CUN threonine. Species shown in black possess mitochondrial  (but not ), and in these organisms CUN codons are assigned to Leu. The yeast species marked red, such as K. thermotolerans, have lost mitochondrial  and obtained  that decodes CUN codons as Thr. K. lactis is marked magenta as it has no CUN codons and no corresponding tRNA with a UAG anticodon. A. gossypii (marked blue) contains a tRNA species with a UAG anticodon, yet its identity of this tRNA and the amino acid reading CUN codons in A. gossypii remain obscure (to be discussed by BFL in Organelle Genetics: Evolution of Organelle Genomes and Gene Expression, Springer 2011).
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Related In: Results  -  Collection

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Figure 3: Phylogeny of yeast species based on concatenated mtDNA-encoded protein sequences. The phylogenetic analysis with PhyloBayes and the CAT model is based on 13 mtDNA encoded proteins. All divergence points are supported by posterior probability values of 1.0, except where indicated. The red arrow points to the concomitant loss of all seven nad genes and the start of mitochondrial codon reassignments, including AUA methionine, CUN threonine. Species shown in black possess mitochondrial (but not ), and in these organisms CUN codons are assigned to Leu. The yeast species marked red, such as K. thermotolerans, have lost mitochondrial and obtained that decodes CUN codons as Thr. K. lactis is marked magenta as it has no CUN codons and no corresponding tRNA with a UAG anticodon. A. gossypii (marked blue) contains a tRNA species with a UAG anticodon, yet its identity of this tRNA and the amino acid reading CUN codons in A. gossypii remain obscure (to be discussed by BFL in Organelle Genetics: Evolution of Organelle Genomes and Gene Expression, Springer 2011).
Mentions: The unsolved question of the yeast mitochondrial CUN codon reassignment is the evolutionary origin of with an 8-nt anticodon loop and a UAG anticodon. To analyze the recruitment, we performed a phylogenetic analysis of all mitochondrial tRNAs of S. cerevisiae and related yeast species using Bayesian inference (Figure 2). Not surprisingly, the 10 organisms with are closely related; yet this cluster is related to tRNAHis (72% sequence identity between the two respective S. cerevisiae tRNAs; Figure 1). In contrast, and are definitively distant in the phylogeny (Figures 2, Supplementary Figure S1) and the respective S. cerevisiae tRNAs share only 52% sequence identity. As the phylogenetic signal in tRNA sequences is limited by the small number of informative sequence sites, and not a reliable marker in species phylogenies because of occasional identity shifts [e.g. (28)], we have built a yeast species tree based on mitochondrion-encoded proteins to permit mapping of evolutionary changes to this tree. The result of this phylogenetic analysis (Figure 3) is consistent with a single origin of the 10 yeast species that have a homolog with an 8-nt anticodon loop, a clade emerging close to the divergence of Kluyveromyces species and subsequent to Pichia canadensis. Together, these results strongly suggest that derived from mitochondrial tRNAHis in an ancestral yeast species.Figure 2.

Bottom Line: A loss of the first nucleotide (G(-1)) in tRNA(His) converts it to a substrate for MST1 with a K(m) value (0.7 μM) comparable to that of (0.3 μM), and addition of G(-1) to allows efficient histidylation by histidyl-tRNA synthetase.We also show that MST1 from Candida albicans, a yeast in which CUN codons remain assigned to leucine, could not threonylate , suggesting that MST1 has coevolved with .Our work provides the first clear example of a recent recoding event caused by alloacceptor tRNA gene recruitment.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA.

ABSTRACT
The standard genetic code is used by most living organisms, yet deviations have been observed in many genomes, suggesting that the genetic code has been evolving. In certain yeast mitochondria, CUN codons are reassigned from leucine to threonine, which requires an unusual tRNA(Thr) with an enlarged 8-nt anticodon loop ( ). To trace its evolutionary origin we performed a comprehensive phylogenetic analysis which revealed that evolved from yeast mitochondrial tRNA(His). To understand this tRNA identity change, we performed mutational and biochemical experiments. We show that Saccharomyces cerevisiae mitochondrial threonyl-tRNA synthetase (MST1) could attach threonine to both and the regular , but not to the wild-type tRNA(His). A loss of the first nucleotide (G(-1)) in tRNA(His) converts it to a substrate for MST1 with a K(m) value (0.7 μM) comparable to that of (0.3 μM), and addition of G(-1) to allows efficient histidylation by histidyl-tRNA synthetase. We also show that MST1 from Candida albicans, a yeast in which CUN codons remain assigned to leucine, could not threonylate , suggesting that MST1 has coevolved with . Our work provides the first clear example of a recent recoding event caused by alloacceptor tRNA gene recruitment.

Show MeSH