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.
Amino acid sequence of reconstructed archaeal ancestral NDK, Arc3nh
Amino acid sequence of Arc3nh, a last archaeal common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model
Arc3nh.txt
Amino acid sequence of reconstructed archaeal ancestral NDK, Arc4nh
Amino acid sequence of Arc4nh, a last archaeal common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model.
Arc4nh.txt
Amino acid sequence of reconstructed archaeal ancestral NDK, Arc6
Amino acid sequence of Arc6, a last archaeal common ancestor of nucleoside diphosphate kinase inferred from a dataset without hyperthermophilic sequences.
Arc6.txt
Amino acid sequence of reconstructed archaeal and bacterial ancestral NDK, ArcBac7
Amino acid sequence of ArcBac7, a last archaeal and bacterial ancestor of nucleoside diphosphate kinase inferred from a dataset without hyperthermophilic sequences.
ArcBac7.txt
Amino acid sequence of reconstructed bacterial ancestral NDK, Bac3nh
Amino acid sequence of Bac3nh, a last bacterial common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model.
Bac3nh.txt
Amino acid sequence of reconstructed bacterial ancestral NDK, Bac4nh
Amino acid sequence of Bac4nh, a last bacterial common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model.
Bac4nh.txt
Amino acid sequence of reconstructed bacterial ancestral NDK, Bac6
Amino acid sequence of Bac6, a last bacterial common ancestor of nucleoside diphosphate kinase inferred from a dataset without hyperthermophilic sequences.
Bac6.txt
Amino acid sequence of reconstructed last universal common ancestral NDK, Com3nh
Amino acid sequence of Com3nh, a last universal common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model.
Com3nh.txt
Amino acid sequence of reconstructed last universal common ancestral NDK, Com4nh
Amino acid sequence of Com4nh, a last universal common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model.
Com4nh.txt