Preservation of the metaproteome: variability of protein preservation in ancient dental calculus

Meaghan Mackie,Jessica Hendy,Abigail D Lowe,Alessandra Sperduti,Malin Holst,Matthew J Collins,Camilla F Speller

doi:10.1080/20548923.2017.1361629

Abstract

ABSTRACTProteomic analysis of dental calculus is emerging as a powerful tool for disease and dietary characterisation of archaeological populations. To better understand the variability in protein results from dental calculus, we analysed 21 samples from three Roman-period populations to compare: 1) the quantity of extracted protein; 2) the number of mass spectral queries; and 3) the number of peptide spectral matches and protein identifications. We found little correlation between the quantity of calculus analysed and total protein identifications, as well as no systematic trends between site location and protein preservation. We identified a wide range of individual variability, which may be associated with the mechanisms of calculus formation and/or post-depositional contamination, in addition to taphonomic factors. Our results suggest dental calculus is indeed a stable, long-term reservoir of proteins as previously reported, but further systematic studies are needed to identify mechanisms associated with protein entrapment and survival in dental calculus.

Highlights

Technological developments in high-resolution tandem mass spectrometry have substantially improved our ability to access and identify proteins from archaeological materials
Archaeological materials Dental calculus was collected from 21 individuals from three sites: two sites located in England (Oxford Street and Driffield Terrace) and one site in Italy (Isola Sacra) (Table 1, Figure 1)
Protein yields from Isola Sacra ranged from 3.24-7.59 μg/mg of calculus while Oxford Street samples ranged from 1.75-9.05 μg/mg of calculus(Figure 2)

Summary

Introduction

Technological developments in high-resolution tandem mass spectrometry have substantially improved our ability to access and identify proteins from archaeological materials. The mineralized matrix of dental calculus is of high physical hardness and durability, preserving organic microscopic debris and biomolecules. Found on skeletal material, calculus has been described as “one of the richest known sources of ancient biomolecules in the archaeological record” (Warinner, et al, 2015), preserving molecular evidence of oral bacteria, the human host, as well as consumed foodstuffs, all of which can be directly tied to the individual (Warinner, et al, 2015; Weyrich, et al, 2015). Studies have already recognised the potential of calculus for increasing our understanding of ancient human microbiomes (Preus, et al, 2011; Adler, et al, 2013; Warinner, et al, 2015), dietary practices (Warinner, et al, 2014b), host genetics (Ozga, et al, 2016), and individual disease processes and immune responses (Warinner, et al, 2014a)

Methods

Results

Discussion

Conclusion