Protein sequences bound to mineral surfaces persist into deep time (original) (raw)

NON-AVIAN DINOSAUR EGGSHELL CALCITE CONTAINS ANCIENT, ENDOGENOUS AMINO ACIDS

bioRxiv, 2020

Rates of peptide bond hydrolysis and other diagenetic reactions are not favourable for Mesozoic protein survival. Proteins hydrolyse into peptide fragments and free amino acids that, in open systems such as bone, can leach from the specimen and be further degraded. However, closed systems are more likely to retain degradation products derived from endogenous proteins. Amino acid racemisation data in experimental and subfossil material suggests that mollusc shell and avian eggshell calcite crystals can demonstrate closed system behaviour, retaining endogenous amino acids. Here, high-performance liquid chromatography reveals that the intra-crystalline fraction of Late Cretaceous (estimated ~80 Ma) titanosaur sauropod eggshell is enriched in some of the most stable amino acids (Glx, Gly, Ala, and possibly Val) and those that racemise are fully racemic, despite being some of the slowest racemising amino acids. These results are consistent with degradation trends deduced from modern, thermally matured, sub-fossil, and ~3.8 Ma avian eggshell, as well as ~30 Ma calcitic mollusc opercula. Selective preservation of certain fully racemic amino acids, which do not racemise in-chain, along with similar concentrations of free versus total hydrolysable amino acids, likely suggests complete hydrolysis of original peptides. Liquid chromatography-tandem mass spectrometry supports this hypothesis by failing to detect any non-contamination peptide sequences from the Mesozoic eggshell. Pyrolysis-gas chromatography-mass spectrometry reveals pyrolysates consistent with amino acids as well as aliphatic hydrocarbon homologues that are not present in modern eggshell, suggestive of kerogen formation deriving from eggshell lipids. Raman spectroscopy yields bands consistent with various organic molecules, possibly including N-bearing molecules or geopolymers. These closed-system amino acids are possibly the most thoroughly supported non-avian dinosaur endogenous protein-derived constituents, at least those that have not undergone oxidative condensation with other classes of biomolecules. Biocrystal matrices can help preserve mobile organic molecules by trapping them (perhaps with the assistance of resistant organic polymers), but trapped organics are nevertheless prone to diagenetic degradation even if such reactions might be slowed in exceptional circumstances. The evidence for complete hydrolysis and degradation of most amino acids in the eggshell raises concern about the validity of reported polypeptide sequences from open-system non-avian dinosaur bone and other Mesozoic fossils.

Non-avian dinosaur eggshell calcite can contain ancient, endogenous amino acids

Geochimica et Cosmochimica Acta, 2023

Proteins are the most stable of the macromolecules that carry genetic information over long periods of time. Closed systems are more likely to retain endogenous proteins or their degradation products. Amino acid racemisation data in experimental and subfossil material suggests that mollusc shell and avian eggshell calcite crystals can demonstrate closed system behaviour, retaining endogenous amino acids. Here, Late Cretaceous (Campanian–Maastrichtian) Argentine titanosaurian sauropod eggshells show dark, organic stains under light microscopy/photography and fluorescence imaging. Raman spectroscopy can yield bands consistent with various organic molecules, possibly including N-bearing molecules or geopolymers. Pyrolysis-gas chromatography-mass spectrometry reveals pyrolysates consistent with amino acids as well as aliphatic hydrocarbon homologues that are not present in modern eggshell, consistent with kerogen formation deriving from eggshell lipids. High-performance liquid chromatography reveals that their intra-crystalline fraction can be enriched in some of the most stable amino acids (Glx, Gly, Ala, and possibly Val) and are fully racemic (despite being some of the slowest racemising amino acids), indicating ancient origin. This preservation varies across localities, but similar ancient amino acid profiles were also observed in Late Cretaceous Spanish titanosaurians from several localities and Chinese putative hadrosaurid eggshell. These amino acid results are consistent with previous studies on degradation trends deduced from modern, thermally matured, sub-fossil, and ∼3.8–6.5 Ma avian eggshell, as well as ∼30 Ma calcitic mollusc opercula. Selective preservation of certain fully racemic amino acids, which do not racemise in-chain, and the concentration of free amino acids suggests likely complete hydrolysis of original peptides. Liquid chromatography-tandem mass spectrometry supports this hypothesis by failing to detect any non-contamination peptide sequences from the Mesozoic eggshell. These closed-system amino acids are possibly the most thoroughly supported non-avian dinosaur endogenous protein-derived constituents, at least those that have not undergone oxidative condensation with other classes of biomolecules. Biocrystal matrices can help preserve mobile organic molecules by trapping them (perhaps with the assistance of resistant organic polymers), but trapped organics are nevertheless prone to diagenetic degradation, even if such reactions might be slowed in exceptional circumstances. Future work should survey fossil biocalcite to determine variability in amino acid preservation.

Proteomes of the past: the pursuit of proteins in paleontology

Expert Review of Proteomics, 2019

Introduction: Despite an extensive published literature, skepticism over the claim of original biochemicals including proteins preserved in the fossil record persists and the issue remains controversial. Workers using many different techniques including mass spectrometry, X-ray, electron microscopy and optical spectroscopic techniques, have attempted to verify proteinaceous or other biochemicals that appear endogenous to fossils found throughout the geologic column. Areas covered: This paper presents a review of the relevant literature published over the last 50 years. A comparative survey of the reported techniques used is also given. Expert opinion: Morphological and molecular investigations show that original biochemistry is geologically extensive, geographically global, and taxonomically wide-ranging. The survival of endogenous organics in fossils remains the subject of widespread and increasing research investigation.