Molecular signatures written in bone proteins of 79 AD victims from Herculaneum and Pompeii

Abstract

An extensive proteomic analysis was performed on a set of 12 bones of human victims of the eruption that in AD 79 rapidly buried Pompeii and Herculaneum, allowing the detection of molecular signatures imprinted in the surviving protein components. Bone collagen survived the heat of the eruption, bearing a piece of individual biological history encoded in chemical modifications. Here we show that the human bone proteomes from Pompeii are more degraded than those from the inhabitants of Herculaneum, despite the latter were exposed to temperatures much higher than those experienced in Pompeii. The analysis of the specimens from Pompeii shows lower content of non-collagenous proteins, higher deamidation level and higher extent of collagen modification. In Pompeii, the slow decomposition of victims' soft tissues in the natural dry-wet hydrogeological soil cycles damaged their bone proteome more than what was experienced at Herculaneum by the rapid vanishing of body tissues from intense heat, under the environmental condition of a permanent waterlogged burial context. Results herein presented are the first proteomic analyses of bones exposed to eruptive conditions, but also delivered encouraging results for potential biomarkers that might also impact future development of forensic bone proteomics.

Figure 1

Overall percentage of deamidation for asparagine and glutamine residues of collagenous bone proteins from Pompeii, Herculaneum, Baia Scalandrone and control (H-162, H-142 from). Error bars represent standard deviation and numbers above each bar represent the number of deamidation sites the data is based on.

Figure 2

Backbone cleavages in collagen alpha 1(I) and collagen alpha 2 (I) in bone samples from Pompeii, Herculaneum, Baia Scalandrone and control (H-162, H-142). Overall occurrence per samples groups (A) and in the single samples (B), evaluated as percentage of peptide-spectrum matches (PSMs) of semitryptic peptides over the total number of peptide-spectrum matches (tryptic plus semitryptic peptides).

Figure 3

Peptide-spectrum matches (PSMs) of “dependent peptides” with mass shifts in the type I collagen chains in the sample groups of Pompeii, Herculaneum, Baia Scalandrone and control samples (H-142, H-162). Mass shifts were selected after filtering with localization probabilities of ≥ 80% for modified peptides and occurrence of detection of DP Cluster Mass ≥ 5 times for each sample. Reported data only include mass shifts corresponding to known oxidative modifications with matching amino acid targets (Unimod, http://www.unimod.org/).

Figure 4

Extent of modified lysine residues, reported as percentage of modified over detected (modified plus unmodified) ones.

Figure 5

Extent of modified arginine residues, reported as percentage of modified over detected (modified plus unmodified) ones.

Figure 6

Extent of modified histidine residues, reported as percentage of modified over detected (modified plus unmodified) ones.

Figure 7

Extent of Cα-Cβ bond cleavage at serine and threonine reported as percentage of modified over detected (modified plus unmodified) residues.

Figure 8

Extent of modified proline residues, reported as percentage of modified over detected (modified plus unmodified) ones.

Figure 9

Comparative analysis of the global “damage signatures” in COL1A1 and COL1A2 from human bones of the different archaeological sites. The figure represents the sum of the average modified/unmodified values of K, R, S, T and P diagenetic modifications (except hydroxyproline and deamidation) at the specific primary structure positions of COL1A1 and COL1A2.

Figure 10

Sequence of biological and taphonomic events concerning the 79 AD human victims from Herculaneum and Pompeii, in comparison with the skeletons from the Baia Scalandrone graveyard.