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

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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.