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Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins

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  • Eric A. Gaucher

    (University of Florida)

  • J. Michael Thomson

    (University of Florida
    University of North Carolina)

  • Michelle F. Burgan

    (University of Florida)

  • Steven A. Benner

    (University of Florida
    University of Florida
    University of Florida)

Abstract

Features of the physical environment surrounding an ancestral organism can be inferred by reconstructing sequences1,2,3,4,5,6,7,8,9 of ancient proteins made by those organisms, resurrecting these proteins in the laboratory, and measuring their properties. Here, we resurrect candidate sequences for elongation factors of the Tu family (EF-Tu) found at ancient nodes in the bacterial evolutionary tree, and measure their activities as a function of temperature. The ancient EF-Tu proteins have temperature optima of 55–65 °C. This value seems to be robust with respect to uncertainties in the ancestral reconstruction. This suggests that the ancient bacteria that hosted these particular genes were thermophiles, and neither hyperthermophiles nor mesophiles. This conclusion can be compared and contrasted with inferences drawn from an analysis of the lengths of branches in trees joining proteins from contemporary bacteria10, the distribution of thermophily in derived bacterial lineages11, the inferred G + C content of ancient ribosomal RNA12, and the geological record combined with assumptions concerning molecular clocks13. The study illustrates the use of experimental palaeobiochemistry and assumptions about deep phylogenetic relationships between bacteria to explore the character of ancient life.

Suggested Citation

  • Eric A. Gaucher & J. Michael Thomson & Michelle F. Burgan & Steven A. Benner, 2003. "Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins," Nature, Nature, vol. 425(6955), pages 285-288, September.
    • Handle: RePEc:nat:nature:v:425:y:2003:i:6955:d:10.1038_nature01977
    DOI: 10.1038/nature01977
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    Cited by:

    1. Paul D Williams & David D Pollock & Benjamin P Blackburne & Richard A Goldstein, 2006. "Assessing the Accuracy of Ancestral Protein Reconstruction Methods," PLOS Computational Biology, Public Library of Science, vol. 2(6), pages 1-8, June.
    2. Zhongyi Lu & Runyue Xia & Siyu Zhang & Jie Pan & Yang Liu & Yuri I. Wolf & Eugene V. Koonin & Meng Li, 2024. "Evolution of optimal growth temperature in Asgard archaea inferred from the temperature dependence of GDP binding to EF-1A," Nature Communications, Nature, vol. 15(1), pages 1-7, December.
    3. Bin Ma & Louxin Zhang, 2011. "Efficient estimation of the accuracy of the maximum likelihood method for ancestral state reconstruction," Journal of Combinatorial Optimization, Springer, vol. 21(4), pages 409-422, May.
    4. Robert K Bradley & Ian Holmes, 2009. "Evolutionary Triplet Models of Structured RNA," PLOS Computational Biology, Public Library of Science, vol. 5(8), pages 1-20, August.

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