Preserved Proteins from Extinct Bison latifrons Identified by Tandem Mass Spectrometry; Hydroxylysine Glycosides are a Common Feature of Ancient Collagen

Ryan C Hill,Matthew J Wither,Travis Nemkov,Alexander Barrett,Angelo D'Alessandro,Monika Dzieciatkowska,Kirk C Hansen

doi:10.1074/mcp.m114.047787

Ryan C Hill, Matthew J Wither + Show 5 more

Open Access

https://doi.org/10.1074/mcp.m114.047787

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Abstract

Bone samples from several vertebrates were collected from the Ziegler Reservoir fossil site, in Snowmass Village, Colorado, and processed for proteomics analysis. The specimens come from Pleistocene megafauna Bison latifrons, dating back ∼ 120,000 years. Proteomics analysis using a simplified sample preparation procedure and tandem mass spectrometry (MS/MS) was applied to obtain protein identifications. Several bioinformatics resources were used to obtain peptide identifications based on sequence homology to extant species with annotated genomes. With the exception of soil sample controls, all samples resulted in confident peptide identifications that mapped to type I collagen. In addition, we analyzed a specimen from the extinct B. latifrons that yielded peptide identifications mapping to over 33 bovine proteins. Our analysis resulted in extensive fibrillar collagen sequence coverage, including the identification of posttranslational modifications. Hydroxylysine glucosylgalactosylation, a modification thought to be involved in collagen fiber formation and bone mineralization, was identified for the first time in an ancient protein dataset. Meta-analysis of data from other studies indicates that this modification may be common in well-preserved prehistoric samples. Additional peptide sequences from extracellular matrix (ECM) and non-ECM proteins have also been identified for the first time in ancient tissue samples. These data provide a framework for analyzing ancient protein signatures in well-preserved fossil specimens, while also contributing novel insights into the molecular basis of organic matter preservation. As such, this analysis has unearthed common posttranslational modifications of collagen that may assist in its preservation over time. The data are available via ProteomeXchange with identifier PXD001827.

Highlights

During the last decade, paleontology and taphonomy have begun to overlap with the field of proteomics to shed new light on preserved organic matter in fossilized bones [1,2,3,4]
Mass spectrometry (MS)-based screening of species-specific collagen peptides has recently been used as a low-cost, rapid alternative to DNA sequencing for taxonomic attribution of morphologically unidentifiable small bone fragments and teeth stemming from diverse archeological contexts [25, 31,32,33]
One of the first direct measurements was by amino acid analysis, which showed that the compositional profile of ancient samples was consistent with collagens in modern bone samples [37,38,39]

Summary

Introduction

Paleontology and taphonomy (the study of decaying organisms over time and the fossilization processes) have begun to overlap with the field of proteomics to shed new light on preserved organic matter in fossilized bones [1,2,3,4]. The presence of glycosylated hydroxylysine residues was identified as a unique feature of bone fossil collagen, as gleaned through meta-analyses of raw data from previous reports on woolly mammoth (Mammuthus primigenius) and bovine samples [29, 30].

Results

Conclusion