Excavating ancient egg shell at Olduvai Gorge, Tanzania by Manuel Domínguez-Rodrigo (CC BY 4.0)

Prehistoric proteins in an eggshell

Protein fragments have been perfectly preserved for 3.8 million years in ostrich eggshells in Africa.

The pattern of chemical reactions that break down the molecules that make our bodies is still fairly mysterious. Archaeologists and geologists hope that dead organisms (or artefacts made from them) might not decay entirely, leaving behind clues to their lives. We know that some molecules are more resistant than others; for example, fats are tough and survive for a long time while DNA is degraded very rapidly. Proteins, which are made of chains of smaller molecules called amino acids, are usually sturdier than DNA. Since the amino acid sequence of a protein reflects the DNA sequence that encodes it, proteins in fossils can help researchers to reconstruct how extinct organisms are related in cases where DNA cannot be retrieved.

Time, temperature, burial environment and the chemistry of the fossil all influence how quickly a protein decays. However, it is not clear what mechanisms slow down decay so that full protein sequences can be preserved and identified after millions of years. As a result, it is difficult to know where to look for these ancient sequences.

In the womb of ostriches, several proteins are responsible for assembling the minerals that make up the ostrich eggshell. These proteins become trapped tightly within the mineral crystals themselves. In this situation, proteins can potentially be preserved over geological time. Beatrice Demarchi and colleagues have now studied 3.8 million-year-old eggshells found close to the equator and, despite the extent to which the samples have degraded, discovered fully preserved protein sequences.

Using a computer simulation method called molecular dynamics, Demarchi and colleagues calculated that the protein sequences that are able to survive the longest are stabilized by strong binding to the surface of the mineral crystals. The authenticity of these sequences was tested thoroughly using a combination of several approaches that Demarchi and colleagues recommend using as a standard for ancient protein studies.

Overall, it appears that biominerals are an excellent source of ancient protein sequences because mineral binding ensures survival. A systematic survey of fossil biominerals from different environments is now needed to assess whether these biomolecules have the potential to act as barcodes for interpreting the evolution of organisms.

To find out more

Read the eLife research paper on which this eLife digest is based: “Protein sequences bound to mineral surfaces persist into deep time” (September 27, 2016).
Read a commentary on this research paper by Adam F Wallace and James D Schiffbauer.
Listen to Matthew Collins talk about ancient ostrich proteins in this episode of the eLife podcast.
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