Protein sequences bound to mineral surfaces persist into deep time

Author:

Demarchi Beatrice1ORCID,Hall Shaun2,Roncal-Herrero Teresa3,Freeman Colin L2,Woolley Jos1,Crisp Molly K4,Wilson Julie45,Fotakis Anna6,Fischer Roman7,Kessler Benedikt M7,Rakownikow Jersie-Christensen Rosa8,Olsen Jesper V8,Haile James9,Thomas Jessica610,Marean Curtis W1112,Parkington John13,Presslee Samantha1,Lee-Thorp Julia9,Ditchfield Peter9,Hamilton Jacqueline F14,Ward Martyn W14,Wang Chunting Michelle14,Shaw Marvin D14,Harrison Terry15,Domínguez-Rodrigo Manuel16,MacPhee Ross DE17,Kwekason Amandus18,Ecker Michaela9ORCID,Kolska Horwitz Liora19,Chazan Michael2021,Kröger Roland3,Thomas-Oates Jane422,Harding John H2,Cappellini Enrico6,Penkman Kirsty4,Collins Matthew J1

Affiliation:

1. BioArCh, Department of Archaeology, University of York, York, United Kingdom

2. Department of Material Science and Engineering, University of Sheffield, Sheffield, United Kingdom

3. Department of Physics, University of York, York, United Kingdom

4. Department of Chemistry, University of York, York, United Kingdom

5. Department of Mathematics, University of York, York, United Kingdom

6. Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark

7. Advanced Proteomics Facility, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom

8. Novo Nordisk Foundation Center for Protein Research, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark

9. Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom

10. Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Bangor, United Kingdom

11. Institute of Human Origins, SHESC, Arizona State University, Tempe, United States

12. Centre for Coastal Palaeoscience, Nelson Mandela Metropolitan University, Port Elizabeth, South Africa

13. Department of Archaeology, University of Cape Town, Cape Town, South Africa

14. Wolfson Atmospheric Chemistry Laboratories, Department of Chemistry, University of York, York, United Kingdom

15. Center for the Study of Human Origins, Department of Anthropology, New York University, New York, United States

16. Department of Prehistory, Complutense University of Madrid, Madrid, Spain

17. Department of Mammalogy, American Museum of Natural History, New York, United States

18. National Museum of Tanzania, Dar es Salaam, Tanzania

19. National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel

20. Department of Anthropology, University of Toronto, Toronto, Canada

21. Evolutionary Studies Institute, University of the Witwatersrand, Braamfontein, South Africa

22. Centre of Excellence in Mass Spectrometry, University of York, New York, United States

Abstract

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).

Funder

Engineering and Physical Sciences Research Council

Natural Environment Research Council

Arts and Humanities Research Council

European Research Council

Novo Nordisk

Danish National Research Foundation

National Science Foundation

Hyde Family Foundations

John Templeton Foundation

Arizona State University

National Geographic Society

Leakey Foundation

Tanzanian Department of Antiquities

Social Sciences and Humanities Research Council of Canada

Leverhulme Trust

Spanish Ministry of Economy and Competitivity

Publisher

eLife Sciences Publications, Ltd

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Medicine,General Neuroscience

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