The diagenetic fate of collagen as revealed by analytical pyrolysis of fossil fish scales from deep time

Abstract

The mechanism of protein degradation has remained a topic of debate (specifically concerning their preservation in deep time), which has recently been invigorated due to multiple published reports of preservation ranging from Miocene to the Triassic that potentially challenge the convention that protein preservation beyond the Cenozoic is extremely uncommon or is expected to be absent altogether, and thus have attracted skepticism. In this paper, we analyze fossil fish scales from the Cretaceous, Jurassic, and Triassic using comprehensive pyrolysis gas chromatography coupled with time‐of‐flight mass spectrometry and compare the pyrolytic products so obtained with a well‐preserved fish scale from Late Pliocene, in an attempt to better understand the effects of diagenesis on protein degradation at the molecular level through deep time. We find that the Pliocene fish scale displays a large number of N‐bearing pyrolytic products, including abundant substituted cyclic 2,5‐diketopiperazines (2,5‐DKPs) which are diagnostic products of peptide and amino acid pyrolysis. We identify N‐bearing compounds in the Mesozoic fish scales—however, among the 2,5‐DKPs that were identified in the Pliocene scale, only diketodipyrrole (or cyclo (Pyr‐Pyr)) is present in the Mesozoic scales. We discuss the implications of N‐bearing pyrolytic products with emphasis on 2,5‐DKPs in geological samples and conclude that the discrepancy in abundance and variety of N‐bearing products between Pliocene and Mesozoic scales indicates that the protein component in the latter has been extensively diagenetically altered, while a suite of DKPs such as in the former would imply stronger evidence to indicate preservation of protein. We conclude that analytical pyrolysis is an effective tool for detecting preservation of intact proteins, as well as for providing insights into their degradation mechanisms, and can potentially be utilized to assign proteinaceous origin to a fossil sample of unknown affinity.

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

“…This implies that the ancient amino acids that were detected using HPLC in the titanosaurian eggshells are indeed free and not secondarily released from covalent bonds from within a recalcitrant organic polymer. Therefore, the formation of N-heterocyclic polymers can lead to a reduction of endogenous amino acids as they are incorporated into the polymer, but can their recalcitrant nature (along with that of kerogen) then trap any remaining thermally stable amino acids (as also suggested by Umamaheswaran et al 2022)? Such a protective capability might offset the likelihood of opening the system as a result of calcite dissolution and recrystallisation.…”

Assembly‐driven protection from hydrolysis as key selective force during chemical evolution

“…For example, the rate of hydrolysis of a particular peptide bond in the ribonuclease T1 enzyme decreases by 1700‐fold upon folding [119]. Protein assemblies can be preserved under environmental conditions for tens of millions of years [120]. Amyloids, which are assemblies characterized by a fibrillar morphology composed of β‐sheet, are associated with various diseases and are known to be highly resistant to hydrolysis [107,121–123].…”