Demongeot Jacques, Seligmann Hervé
Faculty of Medicine, Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, Université Grenoble Alpes, 38700, La Tronche, France.
The National Natural History Collections, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
Acta Biotheor. 2019 Dec;67(4):273-297. doi: 10.1007/s10441-019-09356-w. Epub 2019 Aug 6.
Theoretical minimal RNA rings attempt to mimick life's primitive RNAs. At most 25 22-nucleotide-long RNA rings code once for each biotic amino acid, a start and a stop codon and form a stem-loop hairpin, resembling consensus tRNAs. We calculated, for each RNA ring's 22 potential splicing positions, similarities of predicted secondary structures with tRNA vs. rRNA secondary structures. Assuming rRNAs partly derived from tRNA accretions, we predict positive associations between relative secondary structure similarities with rRNAs over tRNAs and genetic code integration orders of RNA ring anticodon cognate amino acids. Analyses consider for each secondary structure all nucleotide triplets as potential anticodon. Anticodons for ancient, chemically inert cognate amino acids are most frequent in the 25 RNA rings. For RNA rings with primordial cognate amino acids according to tRNA-homology-derived anticodons, tRNA-homology and coding sequences coincide, these are separate for predicted cognate amino acids that presumably integrated late the genetic code. RNA ring secondary structure similarity with rRNA over tRNA secondary structures associates best with genetic code integration orders of anticodon cognate amino acids when assuming split anticodons (one and two nucleotides at the spliced RNA ring 5' and 3' extremities, respectively), and at predicted anticodon location in the spliced RNA ring's midst. Results confirm RNA ring homologies with tRNAs and CDs, ancestral status of tRNA half genes split at anticodons, the tRNA-rRNA axis of RNA evolution, and that single theoretical minimal RNA rings potentially produce near-complete proto-tRNA sets. Hence genetic code pre-existence determines 25 short circular gene- and tRNA-like RNAs. Accounting for each potential splicing position, each RNA ring potentially translates most amino acids, realistically mimicks evolution of the tRNA-rRNA translation machinery. These RNA rings 'of creation' remind the uroboros' (snake biting its tail) symbolism for creative regeneration.
理论上的最小RNA环试图模拟生命的原始RNA。最多25个22个核苷酸长的RNA环为每个生物氨基酸、一个起始密码子和一个终止密码子编码一次,并形成一个茎环发夹结构,类似于共有tRNA。我们针对每个RNA环的22个潜在剪接位置,计算了预测的二级结构与tRNA和rRNA二级结构的相似性。假设rRNA部分源自tRNA的附加,我们预测与rRNA相比,与tRNA的相对二级结构相似性与RNA环反密码子同源氨基酸的遗传密码整合顺序之间存在正相关。分析将每个二级结构中的所有核苷酸三联体视为潜在的反密码子。在这25个RNA环中,古老的、化学惰性同源氨基酸的反密码子最为常见。对于根据tRNA同源性衍生的反密码子具有原始同源氨基酸的RNA环,tRNA同源性和编码序列是一致的,而对于可能在遗传密码中较晚整合的预测同源氨基酸,它们是分开的。当假设分裂反密码子(分别在剪接RNA环的5'和3'末端有一个和两个核苷酸)以及在剪接RNA环中间的预测反密码子位置时,RNA环与rRNA的二级结构相似性与tRNA二级结构相比,与反密码子同源氨基酸的遗传密码整合顺序关联最佳。结果证实了RNA环与tRNA和编码区的同源性、反密码子处分裂的tRNA半基因的祖先状态、RNA进化的tRNA-rRNA轴,以及单个理论最小RNA环可能产生近乎完整的原tRNA集。因此,遗传密码的先存性决定了25个短的环状基因样和tRNA样RNA。考虑到每个潜在的剪接位置,每个RNA环可能翻译大多数氨基酸,切实模拟了tRNA-rRNA翻译机制的进化。这些“创造之环”的RNA让人想起衔尾蛇(蛇咬自己尾巴)象征的创造性再生。