Robustness of predictions of extremely thermally stable proteins in ancient organisms

Satoshi Akanuma, Shin ichi Yokobori, Yoshiki Nakajima, Mizumo Bessho, Akihiko Yamagishi

    Research output: Contribution to journalArticle

    16 Citations (Scopus)

    Abstract

    A number of studies have addressed the environmental temperatures experienced by ancient life. Computational studies using a nonhomogeneous 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 reinferred ancestral sequences using a dataset from which hyperthermophilic sequences were excluded. We also reinferred ancestral sequences using a nonhomogeneous 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.

    Original languageEnglish
    Pages (from-to)2954-2962
    Number of pages9
    JournalEvolution
    Volume69
    Issue number11
    DOIs
    Publication statusPublished - 2015 Nov 1

    Keywords

    • Ancestral sequence reconstruction
    • Nucleoside diphosphate kinase
    • Phylogenetic tree
    • Substitution model
    • Unfolding temperature

    ASJC Scopus subject areas

    • Agricultural and Biological Sciences(all)
    • Ecology, Evolution, Behavior and Systematics
    • Genetics

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  • Cite this

    Akanuma, S., Yokobori, S. I., Nakajima, Y., Bessho, M., & Yamagishi, A. (2015). Robustness of predictions of extremely thermally stable proteins in ancient organisms. Evolution, 69(11), 2954-2962. https://doi.org/10.1111/evo.12779