1. Biochemistry and Chemical Biology
  2. Evolutionary Biology

Survival of mineral-bound peptides into the Miocene

  1. Beatrice Demarchi  Is a corresponding author
  2. Meaghan Mackie
  3. Zhiheng Li
  4. Tao Deng
  5. Matthew J. Collins
  6. Julia Clarke
  1. University of Turin, Italy
  2. University of Copenhagen, Denmark
  3. Chinese Academy of Sciences, China
  4. University of Cambridge, United Kingdom
  5. The University of Texas at Austin, United States
https://doi.org/10.7554/eLife.82849
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  1. Beatrice Demarchi
  2. Meaghan Mackie
  3. Zhiheng Li
  4. Tao Deng
  5. Matthew J. Collins
  6. Julia Clarke
(2022)
Survival of mineral-bound peptides into the Miocene
eLife 11:e82849.
https://doi.org/10.7554/eLife.82849
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Abstract

Previously we showed that authentic peptide sequences could be obtained from 3.8-Ma-old ostrich eggshell (OES) from the site of Laetoli, Tanzania (Demarchi et al., 2016). Here we show that the same sequences survive in a > 6.5 Ma OES recovered from a palaeosteppe setting in northwestern China. The eggshell is thicker than those observed in extant species and consistent with the Liushu Struthio sp. ootaxon. These findings push the preservation of ancient proteins back to the Miocene and highlight their potential for paleontology, paleoecology and evolutionary biology.

Data availability

Tandem mass spectra supporting peptide sequence identification are reported in Figure 3 and Figure 3 - Supplement 1 to 10.Raw mass spectrometry data and results of bioinformatics analysis are available via ProteomeXchange with identifier PXD035872.

The following data sets were generated

Article and author information

Author details

  1. Beatrice Demarchi

    Department of Life Sciences and Systems Biology, University of Turin, Torino, Italy
    For correspondence
    beatrice.demarchi@unito.it
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8398-4409

  2. Meaghan Mackie

    Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
    Competing interests
    The authors declare that no competing interests exist.

  3. Zhiheng Li

    Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Bejing, China
    Competing interests
    The authors declare that no competing interests exist.

  4. Tao Deng

    Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Bejing, China
    Competing interests
    The authors declare that no competing interests exist.

  5. Matthew J. Collins

    McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.

  6. Julia Clarke

    Department of Geological Sciences, The University of Texas at Austin, Austin, United States
    Competing interests
    The authors declare that no competing interests exist.

Funding

Ministry of University and Research - Italy (Young Researchers - Rita Levi Montalcini)

  • Beatrice Demarchi

Danish National Research Foundation (PROTEIOS (DNRF128))

  • Meaghan Mackie
  • Matthew J. Collins

Alexander von Humboldt Foundation

  • Julia Clarke

Jackson School of Geosciences,University of Texas at Austin

  • Julia Clarke

Chinese National Science Foundation

  • Zhiheng Li
  • Tao Deng

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

© 2022, Demarchi et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Beatrice Demarchi
  2. Meaghan Mackie
  3. Zhiheng Li
  4. Tao Deng
  5. Matthew J. Collins
  6. Julia Clarke
(2022)
Survival of mineral-bound peptides into the Miocene
eLife 11:e82849.
https://doi.org/10.7554/eLife.82849

Share this article

https://doi.org/10.7554/eLife.82849

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Further reading

    1. Biochemistry and Chemical Biology
    2. Evolutionary Biology

    Protein sequences bound to mineral surfaces persist into deep time

    Beatrice Demarchi, Shaun Hall ... Matthew J Collins
    Research Article

    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).