Data from: Robustness of predictions of extremely thermally stable proteins in ancient organisms

A number of studies have addressed the environmental temperatures experienced by ancient life. Computational studies using a non-homogeneous evolution model have estimated ancestral G + C contents of ribosomal RNAs and the amino acid compositions of ancestral proteins, generating hypotheses regarding the mesophilic last universal common ancestor. In contrast, our previous study computationally reconstructed ancestral amino acid sequences of nucleoside diphosphate kinases using a homogeneous model and then empirically resurrected the ancestral proteins. The thermal stabilities of these ancestral proteins were equivalent to or greater than those of extant homologous thermophilic proteins, supporting the thermophilic universal ancestor theory. In this study, we re-inferred ancestral sequences using a dataset from which hyperthermophilic sequences were excluded. We also re-inferred ancestral sequences using a non-homogeneous evolution model. The newly reconstructed ancestral proteins are still thermally stable, further supporting the hypothesis that the ancient organisms contained thermally stable proteins and therefore that they were thermophilic.

已有多项研究针对古生物所经历的环境温度展开探讨。采用非均质进化模型的计算研究曾估算核糖体RNA（ribosomal RNAs）的祖先G+C含量，以及祖先蛋白质的氨基酸组成，由此提出了关于嗜温型最后通用共同祖先（last universal common ancestor）的假说。与之相对，本团队此前的研究采用均质进化模型，对核苷二磷酸激酶（nucleoside diphosphate kinases）的祖先氨基酸序列进行了计算重构，随后通过实验手段复活了这些祖先蛋白质。这些祖先蛋白质的热稳定性与现存同源嗜热蛋白质相当，甚至更优，为嗜热通用共同祖先理论提供了支撑。本研究中，我们使用剔除了超嗜热（hyperthermophilic）序列的数据集重新推断祖先序列；同时还采用非均质进化模型，再次完成了祖先序列的推断。本次重构得到的新型祖先蛋白质仍具备热稳定性，进一步佐证了“古生物体内含有热稳定蛋白质，因此其本身为嗜热生物”这一假说。