Earlham Institute, Norwich Research Park, Norwich, United Kingdom.
Department of Biology, University of Oxford, Oxford, United Kingdom.
PLoS Genet. 2023 Oct 5;19(10):e1010913. doi: 10.1371/journal.pgen.1010913. eCollection 2023 Oct.
The genetic code is one of the most highly conserved features across life. Only a few lineages have deviated from the "universal" genetic code. Amongst the few variants of the genetic code reported to date, the codons UAA and UAG virtually always have the same translation, suggesting that their evolution is coupled. Here, we report the genome and transcriptome sequencing of a novel uncultured ciliate, belonging to the Oligohymenophorea class, where the translation of the UAA and UAG stop codons have changed to specify different amino acids. Genomic and transcriptomic analyses revealed that UAA has been reassigned to encode lysine, while UAG has been reassigned to encode glutamic acid. We identified multiple suppressor tRNA genes with anticodons complementary to the reassigned codons. We show that the retained UGA stop codon is enriched in the 3'UTR immediately downstream of the coding region of genes, suggesting that there is functional drive to maintain tandem stop codons. Using a phylogenomics approach, we reconstructed the ciliate phylogeny and mapped genetic code changes, highlighting the remarkable number of independent genetic code changes within the Ciliophora group of protists. According to our knowledge, this is the first report of a genetic code variant where UAA and UAG encode different amino acids.
遗传密码是生命中高度保守的特征之一。只有少数谱系偏离了“通用”遗传密码。在迄今为止报道的少数遗传密码变体中，UAA 和 UAG 密码子几乎总是具有相同的翻译，这表明它们的进化是耦合的。在这里，我们报告了一种新型未培养纤毛虫的基因组和转录组测序，该纤毛虫属于寡膜纤毛门纲，其中 UAA 和 UAG 终止密码子的翻译已改变为指定不同的氨基酸。基因组和转录组分析表明，UAA 被重新分配为编码赖氨酸，而 UAG 被重新分配为编码谷氨酸。我们鉴定了多个具有与重新分配密码子互补反密码子的抑制 tRNA 基因。我们表明，保留的 UGA 终止密码子在编码区域的 3'UTR 中丰富，这表明存在维持串联终止密码子的功能驱动力。使用系统发生基因组学方法，我们重建了纤毛虫的系统发生，并绘制了遗传密码变化，突出显示了原生动物纤毛门组内独立遗传密码变化的显著数量。据我们所知，这是第一个报告 UAA 和 UAG 编码不同氨基酸的遗传密码变体的报告。
