Proteomic Analysis of a Pleistocene Mammoth Femur Reveals More than One Hundred Ancient Bone Proteins

Abstract

We used high-sensitivity, high-resolution tandem mass spectrometry to shotgun sequence ancient protein remains extracted from a 43 000 year old woolly mammoth ( Mammuthus primigenius ) bone preserved in the Siberian permafrost. For the first time, 126 unique protein accessions, mostly low-abundance extracellular matrix and plasma proteins, were confidently identified by solid molecular evidence. Among the best characterized was the carrier protein serum albumin, presenting two single amino acid substitutions compared to extant African ( Loxodonta africana ) and Indian ( Elephas maximus ) elephants. Strong evidence was observed of amino acid modifications due to post-mortem hydrolytic and oxidative damage. A consistent subset of this permafrost bone proteome was also identified in more recent Columbian mammoth ( Mammuthus columbi ) samples from temperate latitudes, extending the potential of the approach described beyond subpolar environments. Mass spectrometry-based ancient protein sequencing offers new perspectives for future molecular phylogenetic inference and physiological studies on samples not amenable to ancient DNA investigation. This approach therefore represents a further step into the ongoing integration of different high-throughput technologies for identification of ancient biomolecules, unleashing the field of paleoproteomics.

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

“…S7). As in other palaeoproteomes, the presence of such semitryptic peptides is not uncommon and is likely the result of protein diagenesis (23,25,(35)(36)(37). In addition, all three spectra contain a hydroxylated proline on the same position (COL10α1 position 135), further demonstrating consistency among our peptide-spectrum matches.…”

“…Fourth, after exclusion of contaminants, protein composition was similar to other nonhominin bone palaeoproteomes (25,26). For these proteins, we observed the presence of additional diagenetic and in vivo posttranslational modifications (SI Appendix, Fig.…”

“…Many of these (keratins, trypsin, bovine CSN2), but not all (COL4α6, UBB, DCD), have previously been reported as contaminants (Fig. 1B, filled triangles) (25). All proteins identified in our extraction blanks have deamidation frequencies that fall into this group, further suggesting that these 14 proteins are contaminants.…”

“…GO annotation analysis further identified a significant group of blood microparticles (GO:00725262) such as albumin (ALB). These proteins have been identified in nonhominin palaeoproteomes as well and are consistently incorporated into the mineralized bone matrix (25,26).…”

Palaeoproteomic Profiling of Conservation Layers on a 14th Century Italian Wall Painting

“…These glycations were possibly caused by the addition of pigment or formed during heating as part of the glue making process, since they do not occur as frequently in the ancient bones. Along with AGEs, Lys carbamylation (potentially caused by urea release during His or Arg decay) and Lys to aminoadipic acid conversion (a marker for protein degradation41 described in some archaeological studies42) were also observed.…”