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

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.

Reviewing Editor

  1. Yonatan Sahle, University of Cape Town, South Africa

Version history

  1. Preprint posted: August 19, 2022 (view preprint)
  2. Received: August 24, 2022
  3. Accepted: December 16, 2022
  4. Accepted Manuscript published: December 19, 2022 (version 1)
  5. Version of Record published: December 30, 2022 (version 2)

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.

Metrics

  • 772
    Page views
  • 119
    Downloads
  • 6
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  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

Further reading

    1. Biochemistry and Chemical Biology
    2. Structural Biology and Molecular Biophysics
    Karolina Honzejkova, Dalibor Kosek ... Tomas Obsil
    Research Article

    Apoptosis signal-regulating kinase 1 (ASK1) is a crucial stress sensor, directing cells toward apoptosis, differentiation, and senescence via the p38 and JNK signaling pathways. ASK1 dysregulation has been associated with cancer and inflammatory, cardiovascular, and neurodegenerative diseases, among others. However, our limited knowledge of the underlying structural mechanism of ASK1 regulation hampers our ability to target this member of the MAP3K protein family towards developing therapeutic interventions for these disorders. Nevertheless, as a multidomain Ser/Thr protein kinase, ASK1 is regulated by a complex mechanism involving dimerization and interactions with several other proteins, including thioredoxin 1 (TRX1). Thus, the present study aims at structurally characterizing ASK1 and its complex with TRX1 using several biophysical techniques. As shown by cryo-EM analysis, in a state close to its active form, ASK1 is a compact and asymmetric dimer, which enables extensive interdomain and interchain interactions. These interactions stabilize the active conformation of the ASK1 kinase domain. In turn, TRX1 functions as a negative allosteric effector of ASK1, modifying the structure of the TRX1-binding domain and changing its interaction with the tetratricopeptide repeats domain. Consequently, TRX1 reduces access to the activation segment of the kinase domain. Overall, our findings not only clarify the role of ASK1 dimerization and inter-domain contacts but also provide key mechanistic insights into its regulation, thereby highlighting the potential of ASK1 protein-protein interactions as targets for anti-inflammatory therapy.

    1. Biochemistry and Chemical Biology
    Jake W Anderson, David Vaisar ... Natalie G Ahn
    Research Article

    Activation of the extracellular signal-regulated kinase-2 (ERK2) by phosphorylation has been shown to involve changes in protein dynamics, as determined by hydrogen-deuterium exchange mass spectrometry (HDX-MS) and NMR relaxation dispersion measurements. These can be described by a global exchange between two conformational states of the active kinase, named ‘L’ and ‘R,’ where R is associated with a catalytically productive ATP-binding mode. An ATP-competitive ERK1/2 inhibitor, Vertex-11e, has properties of conformation selection for the R-state, revealing movements of the activation loop that are allosterically coupled to the kinase active site. However, the features of inhibitors important for R-state selection are unknown. Here, we survey a panel of ATP-competitive ERK inhibitors using HDX-MS and NMR and identify 14 new molecules with properties of R-state selection. They reveal effects propagated to distal regions in the P+1 and helix αF segments surrounding the activation loop, as well as helix αL16. Crystal structures of inhibitor complexes with ERK2 reveal systematic shifts in the Gly loop and helix αC, mediated by a Tyr-Tyr ring stacking interaction and the conserved Lys-Glu salt bridge. The findings suggest a model for the R-state involving small movements in the N-lobe that promote compactness within the kinase active site and alter mobility surrounding the activation loop. Such properties of conformation selection might be exploited to modulate the protein docking interface used by ERK substrates and effectors.