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Nuclear genetic codes with a different meaning of the UAG and the UAA codon

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ABSTRACT

Background: Departures from the standard genetic code in eukaryotic nuclear genomes are known for only a handful of lineages and only a few genetic code variants seem to exist outside the ciliates, the most creative group in this regard. Most frequent code modifications entail reassignment of the UAG and UAA codons, with evidence for at least 13 independent cases of a coordinated change in the meaning of both codons. However, no change affecting each of the two codons separately has been documented, suggesting the existence of underlying evolutionary or mechanistic constraints.

Results: Here, we present the discovery of two new variants of the nuclear genetic code, in which UAG is translated as an amino acid while UAA is kept as a termination codon (along with UGA). The first variant occurs in an organism noticed in a (meta)transcriptome from the heteropteran Lygus hesperus and demonstrated to be a novel insect-dwelling member of Rhizaria (specifically Sainouroidea). This first documented case of a rhizarian with a non-canonical genetic code employs UAG to encode leucine and represents an unprecedented change among nuclear codon reassignments. The second code variant was found in the recently described anaerobic flagellate Iotanema spirale (Metamonada: Fornicata). Analyses of transcriptomic data revealed that I. spirale uses UAG to encode glutamine, similarly to the most common variant of a non-canonical code known from several unrelated eukaryotic groups, including hexamitin diplomonads (also a lineage of fornicates). However, in these organisms, UAA also encodes glutamine, whereas it is the primary termination codon in I. spirale. Along with phylogenetic evidence for distant relationship of I. spirale and hexamitins, this indicates two independent genetic code changes in fornicates.

Conclusions: Our study documents, for the first time, that evolutionary changes of the meaning of UAG and UAA codons in nuclear genomes can be decoupled and that the interpretation of the two codons by the cytoplasmic translation apparatus is mechanistically separable. The latter conclusion has interesting implications for possibilities of genetic code engineering in eukaryotes. We also present a newly developed generally applicable phylogeny-informed method for inferring the meaning of reassigned codons.

Electronic supplementary material: The online version of this article (doi:10.1186/s12915-017-0353-y) contains supplementary material, which is available to authorized users.

No MeSH data available.


Relative codon frequencies in the rhizarian exLh and I. spirale. a Relative codon frequencies in two different groups of genes (for ribosomal proteins and for subunits of the 26S proteasome; listed in Additional file 1: Tables S1A and S1B) in the rhizarian exLh. b Relative codon frequencies in a reference set of genes of I. spirale (listed in Additional file 3: Tables S2A and S2B). The relative codon frequencies are calculated as the percentage of the codon among all occurrences of codons with the same meaning (i.e., coding for the same amino acid or terminating translation)
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Fig3: Relative codon frequencies in the rhizarian exLh and I. spirale. a Relative codon frequencies in two different groups of genes (for ribosomal proteins and for subunits of the 26S proteasome; listed in Additional file 1: Tables S1A and S1B) in the rhizarian exLh. b Relative codon frequencies in a reference set of genes of I. spirale (listed in Additional file 3: Tables S2A and S2B). The relative codon frequencies are calculated as the percentage of the codon among all occurrences of codons with the same meaning (i.e., coding for the same amino acid or terminating translation)

Mentions: Based on these results, we conclude that UAG is the seventh codon for leucine in the rhizarian exLh and does not serve as a stop codon in this organism. This is not without precedent, as the stop-to-leucine UAG reassignment was previously reported from mitochondrial genomes of several green algae of the order Sphaeropleales [22, 28] and of the chytrid fungus Spizellomyces punctatus and its relatives [21]. Interestingly, we noticed striking differences in the UAG codon abundance between certain groups of genes from the rhizarian exLh. In-frame UAG codons were overrepresented in genes encoding components of the 26S proteasome, where the UAG codon was the most abundant codon for leucine (Fig. 3a). In contrast, UAG was the rarest leucine codon in genes for ribosomal proteins. In total, we identified sequences corresponding to 28 ribosomal protein genes of the rhizarian exLh, but 50% of those sequences did not contain any UAG codon, although they all branched with homologs from Rhizaria, most often (11/14) sisters to those from G. vulgaris. Genes for ribosomal proteins are highly expressed and typically exhibit a strong codon usage bias facilitating efficient synthesis of ribosomal proteins [29]. The low abundance of the UAG codon in ribosomal protein genes in the rhizarian exLh thus suggests that this codon is not as efficiently translated as the six standard codons for leucine.Fig. 3


Nuclear genetic codes with a different meaning of the UAG and the UAA codon
Relative codon frequencies in the rhizarian exLh and I. spirale. a Relative codon frequencies in two different groups of genes (for ribosomal proteins and for subunits of the 26S proteasome; listed in Additional file 1: Tables S1A and S1B) in the rhizarian exLh. b Relative codon frequencies in a reference set of genes of I. spirale (listed in Additional file 3: Tables S2A and S2B). The relative codon frequencies are calculated as the percentage of the codon among all occurrences of codons with the same meaning (i.e., coding for the same amino acid or terminating translation)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
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getmorefigures.php?uid=PMC5304391&req=5

Fig3: Relative codon frequencies in the rhizarian exLh and I. spirale. a Relative codon frequencies in two different groups of genes (for ribosomal proteins and for subunits of the 26S proteasome; listed in Additional file 1: Tables S1A and S1B) in the rhizarian exLh. b Relative codon frequencies in a reference set of genes of I. spirale (listed in Additional file 3: Tables S2A and S2B). The relative codon frequencies are calculated as the percentage of the codon among all occurrences of codons with the same meaning (i.e., coding for the same amino acid or terminating translation)
Mentions: Based on these results, we conclude that UAG is the seventh codon for leucine in the rhizarian exLh and does not serve as a stop codon in this organism. This is not without precedent, as the stop-to-leucine UAG reassignment was previously reported from mitochondrial genomes of several green algae of the order Sphaeropleales [22, 28] and of the chytrid fungus Spizellomyces punctatus and its relatives [21]. Interestingly, we noticed striking differences in the UAG codon abundance between certain groups of genes from the rhizarian exLh. In-frame UAG codons were overrepresented in genes encoding components of the 26S proteasome, where the UAG codon was the most abundant codon for leucine (Fig. 3a). In contrast, UAG was the rarest leucine codon in genes for ribosomal proteins. In total, we identified sequences corresponding to 28 ribosomal protein genes of the rhizarian exLh, but 50% of those sequences did not contain any UAG codon, although they all branched with homologs from Rhizaria, most often (11/14) sisters to those from G. vulgaris. Genes for ribosomal proteins are highly expressed and typically exhibit a strong codon usage bias facilitating efficient synthesis of ribosomal proteins [29]. The low abundance of the UAG codon in ribosomal protein genes in the rhizarian exLh thus suggests that this codon is not as efficiently translated as the six standard codons for leucine.Fig. 3

View Article: PubMed Central - PubMed

ABSTRACT

Background: Departures from the standard genetic code in eukaryotic nuclear genomes are known for only a handful of lineages and only a few genetic code variants seem to exist outside the ciliates, the most creative group in this regard. Most frequent code modifications entail reassignment of the UAG and UAA codons, with evidence for at least 13 independent cases of a coordinated change in the meaning of both codons. However, no change affecting each of the two codons separately has been documented, suggesting the existence of underlying evolutionary or mechanistic constraints.

Results: Here, we present the discovery of two new variants of the nuclear genetic code, in which UAG is translated as an amino acid while UAA is kept as a termination codon (along with UGA). The first variant occurs in an organism noticed in a (meta)transcriptome from the heteropteran Lygus hesperus and demonstrated to be a novel insect-dwelling member of Rhizaria (specifically Sainouroidea). This first documented case of a rhizarian with a non-canonical genetic code employs UAG to encode leucine and represents an unprecedented change among nuclear codon reassignments. The second code variant was found in the recently described anaerobic flagellate Iotanema spirale (Metamonada: Fornicata). Analyses of transcriptomic data revealed that I. spirale uses UAG to encode glutamine, similarly to the most common variant of a non-canonical code known from several unrelated eukaryotic groups, including hexamitin diplomonads (also a lineage of fornicates). However, in these organisms, UAA also encodes glutamine, whereas it is the primary termination codon in I. spirale. Along with phylogenetic evidence for distant relationship of I. spirale and hexamitins, this indicates two independent genetic code changes in fornicates.

Conclusions: Our study documents, for the first time, that evolutionary changes of the meaning of UAG and UAA codons in nuclear genomes can be decoupled and that the interpretation of the two codons by the cytoplasmic translation apparatus is mechanistically separable. The latter conclusion has interesting implications for possibilities of genetic code engineering in eukaryotes. We also present a newly developed generally applicable phylogeny-informed method for inferring the meaning of reassigned codons.

Electronic supplementary material: The online version of this article (doi:10.1186/s12915-017-0353-y) contains supplementary material, which is available to authorized users.

No MeSH data available.