Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.
Institute of Cardiometabolism and Nutrition, Hôpital de la Pitié-Salpêtrière, 47 boulevard de l'Hôpital, 75013 Paris, France.
Nucleic Acids Res. 2018 Mar 16;46(5):2197-2203. doi: 10.1093/nar/gky045.
The position 34 of a tRNA is always modified for efficient recognition of codons and accurate integration of amino acids by the translation machinery. Here, we report genomics features of a deep-sea gut symbiotic Spiroplasma, which suggests that the organism does not require tRNA(34) anticodon modifications. In the genome, there is a novel set of tRNA genes composed of 32 species for recognition of the 20 amino acids. Among the anticodons of the tRNAs, we witnessed the presence of both U34- and C34-containing tRNAs required to decode NNR (A/G) 2:2 codons as countermeasure of probable loss of anticodon modification genes. In the tRNA fragments detected in the gut transcriptome, mismatches expected to be caused by some tRNA modifications were not shown in their alignments with the corresponding genes. However, the probable paucity of modified anticodons did not fundamentally change the codon usage pattern of the Spiroplasma. The tRNA gene profile that probably resulted from the paucity of tRNA(34) modifications was not observed in other symbionts and deep-sea bacteria, indicating that this phenomenon was an evolutionary dead-end. This study provides insights on co-evolution of translation machine and tRNA genes and steric constraints of codon-anticodon interactions in deep-sea extreme environment.
tRNA 的第 34 位总是被修饰，以提高对密码子的识别效率，并使翻译机器准确整合氨基酸。在这里，我们报告了一种深海肠道共生螺旋体的基因组学特征，这表明该生物不需要 tRNA(34)反密码子修饰。在基因组中，有一组新的 tRNA 基因，由 32 个物种组成，用于识别 20 种氨基酸。在这些 tRNA 的反密码子中，我们看到了既含有 U34 又含有 C34 的 tRNA，这是为了解码 NNR(A/G)2:2 密码子而采取的措施，因为可能失去了反密码子修饰基因。在肠道转录组中检测到的 tRNA 片段中，与其相应基因比对时，并没有显示出预期由某些 tRNA 修饰引起的不匹配。然而，缺乏修饰的反密码子并没有从根本上改变螺旋体的密码子使用模式。在其他共生体和深海细菌中没有观察到可能由于 tRNA(34)修饰缺乏而导致的 tRNA 基因谱，这表明这种现象是进化的死胡同。这项研究提供了关于翻译机器和 tRNA 基因的共同进化以及深海极端环境中密码子-反密码子相互作用的空间限制的见解。
