Nucleotide sequence of a yeast mitochondrial threonine‐tRNA able to decode the C—U—N leucine codons

Sibler, Annie-Paule; Dirheimer, G.; Martin, Robert P.

doi:10.1016/0014-5793(81)81194-5

Cited by 21 publications

(13 citation statements)

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“…MST1 could also threonylate , which was unexpected as it was previously thought that a second mitochondrial ThrRS was responsible for aminoacylation. Steady-state kinetic experiments revealed that Sc MST1 recognized and with high affinity, with K m values of 0.29 and 0.44 µM, respectively (Table 1), suggesting that tRNA modifications (17) are not critical for MST1 recognition. These data, together with previous in vivo results, establishes unequivocally that is indeed threonylated by MST1.…”

Section: Resultsmentioning

confidence: 99%

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

Lieberman

Lang

et al. 2011

Nucleic Acids Research

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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 tRNAThr 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 tRNAHis. 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 tRNAHis. A loss of the first nucleotide (G−1) in tRNAHis converts it to a substrate for MST1 with a Km 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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Section: Resultsmentioning

confidence: 99%

“…Three decades after this discovery it is still a mystery how the unusual emerged in the mitochondrial genome. Previous hypotheses suggest that might have evolved from , or alternatively from the missing (11,17,18). However, both hypotheses lack convincing experimental evidence.…”

Section: Introductionmentioning

confidence: 99%

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

Lieberman

Lang

et al. 2011

Nucleic Acids Research

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“…The six species followed by a superscript a in Table 3 have undergone a reassignment of the CUN family to Thr. These species possess an unusual tRNA-Thr with anticodon UAG (Sibler et al 1981; Osawa et al 1990) and the usual tRNA-Leu(UAG) is not found in the genome. In K. lactis , the codon family is not used at all.…”

Section: Reassignments That Can Be Explained By Codon Disappearancementioning

confidence: 99%

The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

2007

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Abstract. Many cases of nonstandard genetic codes are known in mitochondrial genomes. We carry out analysis of phylogeny and codon usage of organisms for which the complete mitochondrial genome is available, and we determine the most likely mechanism for codon reassignment in each case. Reassignment events can be classified according to the gain-loss framework. The ''gain'' represents the appearance of a new tRNA for the reassigned codon or the change of an existing tRNA such that it gains the ability to pair with the codon. The ''loss'' represents the deletion of a tRNA or the change in a tRNA so that it no longer translates the codon. One possible mechanism is codon disappearance (CD), where the codon disappears from the genome prior to the gain and loss events. In the alternative mechanisms the codon does not disappear. In the unassigned codon mechanism, the loss occurs first, whereas in the ambiguous intermediate mechanism, the gain occurs first. Codon usage analysis gives clear evidence of cases where the codon disappeared at the point of the reassignment and also cases where it did not disappear. CD is the probable explanation for stop to sense reassignments and a small number of reassignments of sense codons. However, the majority of sense-to-sense reassignments cannot be explained by CD. In the latter cases, by analysis of the presence or absence of tRNAs in the genome and of the changes in tRNA sequences, it is sometimes possible to distinguish between the unassigned codon and the ambiguous intermediate mechanisms. We emphasize that not all reassignments follow the same scenario and that it is necessary to consider the details of each case carefully.

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“…This example is the reassignment of CUN codons from Leu to Thr in the mitochondria of Saccharomyces cerevisiae (21,22), which belongs to a group of yeast species (Saccharomycetaceae) that lost all seven standard mitochondrial genes encoding subunits of the NADH dehydrogenase complex. Responsible for the reassignment event in the remaining eight protein-coding genes of S. cerevisiae is an unusual with a UAG anticodon (23), and an 8- rather than 7-nt-long anticodon loop, which has evolved from a tRNA His ancestor (21). Here, we report a second instance in which a tRNA closely related to reassigns CUU and CUA codons in the mitochondrial genome of the yeast A .…”

Section: Introductionmentioning

confidence: 99%

Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria

Ling¹,

Daoud²,

Lajoie³

et al. 2013

Nucleic Acids Research

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The discovery of diverse codon reassignment events has demonstrated that the canonical genetic code is not universal. Studying coding reassignment at the molecular level is critical for understanding genetic code evolution, and provides clues to genetic code manipulation in synthetic biology. Here we report a novel reassignment event in the mitochondria of Ashbya (Eremothecium) gossypii, a filamentous-growing plant pathogen related to yeast (Saccharomycetaceae). Bioinformatics studies of conserved positions in mitochondrial DNA-encoded proteins suggest that CUU and CUA codons correspond to alanine in A. gossypii, instead of leucine in the standard code or threonine in yeast mitochondria. Reassignment of CUA to Ala was confirmed at the protein level by mass spectrometry. We further demonstrate that a predicted is transcribed and accurately processed in vivo, and is responsible for Ala reassignment. Enzymatic studies reveal that is efficiently recognized by A. gossypii mitochondrial alanyl-tRNA synthetase (AgAlaRS). AlaRS typically recognizes the G3:U70 base pair of tRNAAla; a G3A change in Ashbya abolishes its recognition by AgAlaRS. Conversely, an A3G mutation in Saccharomyces cerevisiae confers tRNA recognition by AgAlaRS. Our work highlights the dynamic feature of natural genetic codes in mitochondria, and the relative simplicity by which tRNA identity may be switched.

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Nucleotide sequence of a yeast mitochondrial threonine‐tRNA able to decode the C—U—N leucine codons

Cited by 21 publications

References 21 publications

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

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

The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes

Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria

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