Protein sequences bound to mineral surfaces persist into deep time
Beatrice Demarchi Shaun Hall Teresa Roncal-Herrero Colin L Freeman Jos Woolley Molly K Crisp Julie Wilson Anna Fotakis Roman Fischer Benedikt M Kessler Rosa Rakownikow Jersie-Christensen Jesper V Olsen James Haile Jessica Thomas Curtis W Marean John Parkington Samantha Presslee Julia Lee-Thorp Peter Ditchfield Jacqueline F Hamilton Martyn W Ward Chunting Michelle Wang Marvin D Shaw Terry Harrison Manuel Domínguez-Rodrigo Ross DE MacPhee Amandus Kwekason Michaela Ecker Liora Kolska Horwitz Michael Chazan Roland Kröger Jane Thomas-Oates John H Harding Enrico Cappellini Kirsty Penkman Matthew J Collins
University of York, United Kingdom; University of Sheffield, United Kingdom; University of Copenhagen, Denmark; University of Oxford, United Kingdom; Bangor University, United Kingdom; Arizona State University, United States; Nelson Mandela Metropolitan University, South Africa; University of Cape Town, South Africa; New York University, United States; Complutense University of Madrid, Spain; American Museum of Natural History, United States; National Museum of Tanzania, Tanzania; The Hebrew University, Israel; University of Toronto, Canada; University of the Witwatersrand, South Africa; Centre of Excellence in Mass Spectrometry, University of York, United States
Published September 27, 2016
Cite as eLife 2016;5:e17092
Eggshell peptide sequences from Africa have thermal ages two orders of magnitude older than those reported for DNA or bone collagen.
(A) Sites reporting the oldest DNA and collagen sequences are from high latitude sites compared to ostrich eggshell samples from sites in Africa illustrated in (B) for which the current mean annual air temperatures are much higher. (C) Kinetic estimates of rates of decay for DNA (Lindahl and Nyberg, 1972), collagen (Buckley and Collins, 2011) and ostrich eggshell proteins (Crisp et al., 2013) were used to estimate thermal age assuming a constant 10°C (Figure 1—source data 1; Appendix 1. For Elands Bay Cave and Pinnacle Point the oldest samples are shown). Note log scale on the z-axis: struthiocalcin-1 peptide survival is two orders of magnitude greater than any previously reported sequence, offering scope for the survival of peptide sequences into deep time.
Proteins persist longer in the fossil record than DNA, but the longevity, survival mechanisms and substrates remain contested. Here, we demonstrate the role of mineral binding in preserving the protein sequence in ostrich (Struthionidae) eggshell, including from the palaeontological sites of Laetoli (3.8 Ma) and Olduvai Gorge (1.3 Ma) in Tanzania. By tracking protein diagenesis back in time we find consistent patterns of preservation, demonstrating authenticity of the surviving sequences. Molecular dynamics simulations of struthiocalcin-1 and -2, the dominant proteins within the eggshell, reveal that distinct domains bind to the mineral surface. It is the domain with the strongest calculated binding energy to the calcite surface that is selectively preserved. Thermal age calculations demonstrate that the Laetoli and Olduvai peptides are 50 times older than any previously authenticated sequence (equivalent to ~16 Ma at a constant 10°C).
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. Demarchi et al. 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 et al. 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 et al. 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.