Wadsworth Caroline, Procopio Noemi, Anderung Cecilia, Carretero José-Miguel, Iriarte Eneko, Valdiosera Cristina, Elburg Rengert, Penkman Kirsty, Buckley Michael
Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK.
Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.
J Proteomics. 2017 Mar 31;158:1-8. doi: 10.1016/j.jprot.2017.01.004. Epub 2017 Jan 14.
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.
Ancient 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.
古代DNA（aDNA）是从考古遗址的骨骼遗骸中提取的最具信息价值的生物分子，但其保存情况不可预测，提取和分析耗时、昂贵且常常失败。几种为更好地理解aDNA保存情况而提出的方法是基于对蛋白质保存某些方面的表征，但这些方法通常不具有特异性；蛋白质组学分析可能为理解保存过程提供一种有吸引力的方法。在本研究中，对来自多个欧洲考古遗址的69个考古牛骨和牙本质样本进行了深入的蛋白质组学（液相色谱-轨道阱质谱/质谱）分析，并与线粒体aDNA和氨基酸消旋化（AAR）数据进行了比较。这些数据的比较，包括对七种选定非胶原蛋白相对丰度的估计，表明骨或牙本质中aDNA的保存可能与某些蛋白质的保存相关，并且蛋白质组复杂性比蛋白质丰度或AAR更能有效预测aDNA的保存情况。aDNA回收率与蛋白质组丰度之间缺乏强相关性可能表明，aDNA的保存与其与骨羟基磷灰石晶体结合的能力而非与蛋白质结合的能力更为密切相关。
即使在基因组学和蛋白质组学的“组学”技术取得了巨大进步的情况下，古代生物分子的保存情况仍知之甚少。本研究调查了古代DNA与蛋白质的保存关系，考虑了蛋白质组复杂性和相对蛋白质丰度，以增进我们对保存机制的理解。结果表明，虽然蛋白质丰度不一定与aDNA保存直接相关，但蛋白质组复杂性似乎与之相关。
