National Natural History Museum Collections, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel; Department of Life Sciences, Ben Gurion University, 84105 Beer Sheva, Israel.
J Theor Biol. 2014 Jan 7;340:155-63. doi: 10.1016/j.jtbi.2013.08.030. Epub 2013 Sep 4.
The hypothesis that tRNA sidearm loops bear anticodons assumes crossovers between anticodon and sidearms, or translation by expressed aminoacylated tRNA halves forming single stem-loops. Only the latter might require ribosomal adaptations. Drosophila mitochondrial codon usages coevolve with sidearm numbers bearing matching putative anticodons (comparing different codon families in one genome, macroevolution) and when comparing different genomes for single codon families (microevolution). Coevolution between Drosophila and yeast mitochondrial antisense tRNAs and codon usages partly confounds microevolutionary patterns for putative sidearm anticodons. Some tRNA sidearm loops have more than seven nucleotides, putative expanded anticodons potentially matching quadruplet codons (tetracodons, codons expanded by a fourth silent position, forming tetragenes (predicted by alignment analyses of Drosophila mitochondrial genomes)). Tetracodon numbers coevolve with expanded tRNA sidearm loops. Sidearm coevolution with amino acid usages and tetragenes occurs for putative anticodons in 5' and 3' sidearms loops (D and TΨC loops, respectively), are stronger for the D-loop. Results slightly favour isolated stem-loops upon crossover hypotheses. An alternative hypothesis, that patterns observed for sidearm 'anticodons' do not imply translational activity, but recognition signals for tRNA synthetases that aminoacylate tRNAs, is incompatible with tetracodon/tetra-anticodon coevolution. Hence analyses strengthen translational hypotheses for tRNA sidearm anticodons, tetragenes, and antisense tRNAs.
该假设认为 tRNA 侧臂环携带反密码子，假设反密码子和侧臂之间存在交叉，或者通过表达的氨酰化 tRNA 半体形成单茎环进行翻译。只有后者可能需要核糖体适应。果蝇线粒体密码子的使用与携带匹配的假反密码子的侧臂数量共同进化（在一个基因组中比较不同的密码子家族，宏观进化），并且当比较不同基因组中单一密码子家族时（微观进化）。果蝇和酵母线粒体反义 tRNA 与密码子使用之间的共同进化部分混淆了假侧臂反密码子的微观进化模式。一些 tRNA 侧臂环具有超过七个核苷酸，潜在的扩展反密码子可能与四联体密码子匹配（四核苷酸，通过第四位沉默位置扩展的密码子，形成四基因（通过果蝇线粒体基因组的比对分析预测））。四核苷酸数量与扩展的 tRNA 侧臂环共同进化。侧臂与氨基酸使用和四基因的共同进化发生在 5'和 3'侧臂环（D 和 TΨC 环，分别）中的假反密码子中，在 D 环中更强。结果略微倾向于交叉假设中的孤立茎环。另一种假设是，观察到的侧臂“反密码子”模式并不意味着翻译活性，而是氨酰化 tRNA 的 tRNA 合成酶的识别信号，与四核苷酸/四反密码子共同进化不兼容。因此，分析加强了 tRNA 侧臂反密码子、四基因和反义 tRNA 的翻译假说。
