Abstract
Ancient DNA (aDNA) is the most informative biomolecule extracted from skeletal remains at archaeological sites, but its survival is unpredictable and its extraction and analysis is time consuming, expensive and often fails. Several proposed methods for better understanding aDNA survival are based upon the characterisation of some aspect of protein survival, but these are typically non-specific; proteomic analyses may offer an attractive method for understanding preservation processes. In this study, in-depth proteomic (LC-Orbitrap-MS/MS) analyses were carried out on 69 archaeological bovine bone and dentine samples from multiple European archaeological sites and compared with mitochondrial aDNA and amino acid racemisation (AAR) data. Comparisons of these data, including estimations of the relative abundances for seven selected non-collagenous proteins, indicate that the survival of aDNA in bone or dentine may correlate with the survival of some proteins, and that proteome complexity is a more useful predictor of aDNA survival than protein abundance or AAR. The lack of a strong correlation between the recovery of aDNA and the proteome abundance may indicate that the survival of aDNA is more closely linked to its ability to associate with bone hydroxyapatite crystals rather than to associate with proteins. SignificanceAncient biomolecule survival remains poorly understood, even with great advancements in ‘omics’ technologies, both in genomics and proteomics. This study investigates the survival of ancient DNA in relation to that of proteins, taking into account proteome complexity and the relative protein abundances to improve our understanding of survival mechanisms. The results show that although protein abundance is not necessarily directly related to aDNA survival, proteome complexity appears to be.
Highlights
In the last two decades the field of biomolecular archaeology has rapidly expanded, and nowadays genomics and proteomics as well as other omics techniques are frequently applied to archaeology studies [1,2]
As there are many different non-collagenous bone proteins (NCPs) found in all samples, this study will focus on seven selected proteins: fetuin-A, prothrombin, pigment epithelium-derived factor (PEDF), lumican, chondroadherin (CHAD), secreted phosphoprotein 24 (SPP24) and matrix metalloproteinase-20 (MMP20), which have been commonly identified in ancient bone in other studies [31,32] and which have different biological functions and properties
Proteomics can be a useful tool in the analysis of ancient bone and teeth, this study has proved that this technique, in its current form, is unlikely to be useful as a screening method to determine whether a sample is likely to contain ancient DNA (aDNA)
Summary
In the last two decades the field of biomolecular archaeology has rapidly expanded, and nowadays genomics and proteomics as well as other omics techniques are frequently applied to archaeology studies [1,2]. Analysis of ancient DNA (aDNA) is increasingly used worldwide, partly due to the advent of Generation Sequencing (NGS) technologies that have overcome some of the former limitations of aDNA (such as fragmentation, low copy number, damage and contamination). C. Wadsworth et al / Journal of Proteomics 158 (2017) 1–8 understanding the molecular taphonomy of ancient bones and teeth through biomolecules (and proteins given their role in bone structure) will build our knowledge of how degradation/preservation of organic material occurs within the archaeological record. We present for the first time a direct comparison of the ancient proteome and aDNA in bones from four different environments in a total of 69 ancient cattle samples as a means to investigate whether ancient protein survival is a useful biomarker for aDNA preservation
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