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Scientific Method / Science & Exploration

Resurrected proteins reveal details of the ancient earth

Researchers reconstruct the proteins of the ancestors of modern bacteria, …

One of the strengths of science is its internal consistency. It's one thing for geology to tell us where and when continents have collided; it's another entirely when fossil and modern biogeography reveal that the distribution of species reflects those collisions. Some data that appeared in yesterday's Nature helps bring that sort of internal consistency to another aspect of early-earth geology. Researchers have reconstructed proteins that were likely to have been used billions of years ago by the ancestors of modern bacteria and have found that these proteins provide estimates of the early earth's temperatures that match those generated by geologists.

The geologists have measured isotope ratios in ancient ocean sediments to infer the temperatures that prevailed at the times they were deposited. These estimates suggest that the oceans started out hot—over 60°C at 3.5 billion years ago—but gradually cooled to something closer to modern temperatures before the Precambrian glaciations. These figures, however, are subject to a variety of potential errors and have remained controversial.

Enter biology. EF-Tu is a protein essential to all known forms of life; it's used in the manufacture of new proteins by the cell. Because of this central role, EF-Tu activity is finely tuned to the organism's environment, such that the protein is most stable at temperatures near those found in an organism's typical environment. Thus, organisms living in hot springs have an EF-Tu that's stable up to 70°C, while those living in the ocean might have a form that's only stable up to 30°C.

The researchers involved in this study used phylogenetic information from dozens of bacteria to reconstruct various ancestral forms of EF-Tu, going all the way back to the last common ancestor of bacteria. They then produced and purified these proteins, and tested their thermal stability by checking the temperature at which they lost their structure (the melting temperature, or Tm). The results revealed a trend that matched well with the geology, as the oldest EF-Tu proteins had Tms over 60°C, while more recent ancestral proteins had Tms in the 30s and 40s.

There are a lot of statistical issues with reconstructing ancient proteins, but the authors did a number of experiments designed to show that these results are robust. The same trend appeared when a proposed alternative phylogenetic tree was used. The authors also redid the reconstruction using an estimation of the ancestral amino acid use frequencies, as well as with a set of sequences chosen for their wide distribution across a weighted average of potential sequences. None of these differed from their original results by more than a few degrees, suggesting that the work was not a statistical fluke.

This isn't conclusive evidence of global conditions. As the authors note, it's entirely possible that life started out restricted to hot environments, and only gradually spread to the colder areas of the globe. But the close agreement between this data and the geology would seem to argue otherwise.

Nature, 2008. DOI: 10.1038/nature06510

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