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

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.

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Figure 1: The two unrooted universal trees used to reconstruct ancestral bacterial sequences.
Figure 2: Comparisons of reconstructed ancestral sequences.
Figure 3: GDP-binding assay to test thermostability of ancestral and modern EF proteins.

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Acknowledgements

We thank M. Miyamoto, J. Aris, A. Falcon, S. Sassi, C. West and Z. Yang for discussions and assistance with our research. We also thank C. Knudson and A. M. Sanangelantoni for providing EF clones. Funding is provided by the National Research Council and NASA's Astrobiology Institute (E.A.G.), and the NIH and NASA (S.A.B.).

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Correspondence to Eric A. Gaucher.

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Supplementary information

41586_2003_BFnature01977_MOESM1_ESM.doc

Supplementary Figure: Multiple sequence alignment of the three reconstructed ancestral sequences juxtaposed to EF from modern E. coli. Asterisks, colons, and periods indicate identical, highly conserved, and moderately conserved positions, respectively. Sites are colored according to amino acid side chain physiochemical properties. (DOC 29 kb)

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Gaucher, E., Thomson, J., Burgan, M. et al. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425, 285–288 (2003). https://doi.org/10.1038/nature01977

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