Crammed, ambiguous genetic codes. Ambiguous genetic codes

In most nuclear genomes the genetic code appears frozen and largely unambiguous. For unknown reasons, among all eukaryotes, ciliates demonstrate a proclivity for reassigning the standard nuclear stop codons to amino acids, with seven variant genetic codes, including three new ones reported here. The key question is therefore: why is the nuclear genetic code so exceedingly stable in most eukaryotes, but not in ciliates? In ciliates, we have discovered the most sophisticated nuclear genetic codes, which paradoxically translate all 64 codons as standard amino acids, and recognize either one or all three stop codons. "Stop" codon depletion shortly before coding sequence ends suggests mRNA 3' ends are involved in stop/sense disambiguation. We propose that, together with stop codon depletion, ambiguity tolerance, including during stop codon readthrough, has enabled repeated genetic code diversification. Please note that the C. magnum genome assembly contains sequences both ciliate and resident bacterial sequences.

在绝大多数细胞核基因组中，遗传密码呈现出近乎固化且高度明确的特征。然而在所有真核生物中，纤毛虫类（Ciliates）出于未知原因，表现出将标准细胞核终止密码子重分配为氨基酸编码的倾向，目前已发现七种变异遗传密码，其中三种为本文首次报道。因此核心问题随之而来：为何绝大多数真核生物的细胞核遗传密码极为稳定，而纤毛虫类却并非如此？在纤毛虫类中，我们发现了迄今最为精妙的细胞核遗传密码体系：矛盾的是，这类密码子可将全部64个密码子均编码为标准氨基酸，却仅识别1个或全部3个终止密码子。在编码序列末端附近出现的终止密码子缺失现象，暗示信使RNA（mRNA）的3'端参与了终止密码子与编码密码子的歧义消除过程。我们提出，终止密码子缺失与包括终止密码子通读在内的歧义耐受性，共同促成了纤毛虫类遗传密码的多次多样化演化。请注意，巨纤毛虫（C. magnum）的基因组组装序列同时包含纤毛虫来源序列与定植细菌序列。