Dataset Information

Multi-protease analysis of Pleistocene bone proteomes

ABSTRACT: Palaeoproteomics of skeletal tissues has the potential to provide new insights into the evolutionary relationships between globally distributed hominin fossils across the Pleistocene. The use of alternative or additional proteases has the potential to increase both proteome size and protein. However, the potential of alternative proteases beside trypsin remains unexplored systematically in palaeoproteomic studies. Here, we present a comparison of the bone proteome size and protein sequence recovery of six different proteases from four Pleistocene bone specimens. We observe that the majority of the preserved bone proteome is inaccessible to trypsin. We also note that for proteins recovered consistently across several proteases, protein sequence coverage can be increased significantly by combining peptide identifications from two or more proteases. Our results thereby demonstrate that the proteolysis of Pleistocene proteomes by several proteases has clear advantages when addressing evolutionary questions in palaeoproteomics.

INSTRUMENT(S): Q Exactive HF-X

ORGANISM(S): Equidae Homo

TISSUE(S): Bone

SUBMITTER: Frido Welker

LAB HEAD: Enrico Cappellini

PROVIDER: PXD018264 | Pride | 2020-10-13

REPOSITORIES: Pride

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Publications

Multi-protease analysis of Pleistocene bone proteomes.

Lanigan Liam T LT Mackie Meaghan M Feine Susanne S Hublin Jean-Jacques JJ Schmitz Ralf W RW Wilcke Arndt A Collins Matthew J MJ Cappellini Enrico E Olsen Jesper V JV Taurozzi Alberto J AJ Welker Frido F

Journal of proteomics 20200709

Ancient protein analysis is providing new insights into the evolutionary relationships between hominin fossils across the Pleistocene. Protein identification commonly relies on the proteolysis of a protein extract using a single protease, trypsin. As with modern proteome studies, alternative or additional proteases have the potential to increase both proteome size and protein sequence recovery. This could enhance the recovery of phylogenetic information from ancient proteomes. Here we identify 1 ...[more]

PMID: 32652221

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Project description:Pleistocene Pongo teeth show substantial variation in size and morphology, fueling taxonomic debates about the paleodiversity of the genus. We investigated prominent features of the enamel-dentine-junction junction (EDJ) – phylogenetically informative internal structures – of 71 fossil Pongo lower molars from various sites by applying geometric morphometrics and conducted paleoproteomic analyses from enamel proteins to attempt to identify extinct orangutan species. Forty-three orangutan lower molars representing Pongo pygmaeus and Pongo abelii were included for comparison. The shape of the EDJ was analyzed by placing five landmarks on the tip of the main dentine horns, and 142 semilandmarks along the marginal ridges connecting the dentine horns. Paleoproteomic analyses were conducted on 15 teeth of Late Pleistocene Pongo using high-resolution tandem mass spectrometry. The geometric morphometric results show variations in EDJ shape regarding aspects of the height and position of the dentine horns and connecting ridges. Despite the issue of molar position and sample size, modern molars are distinguished from fossil counterparts by their elongated tooth outline and narrowly positioned dentine horns. Proteomic results show that neither a distinction of P. pygmaeus and P. abelii, nor a consistent allocation of fossil specimens to extant species is feasible. Based on the EDJ shape, the (late) Middle to Late Pleistocene Pongo samples from Vietnam share the same morphospace, supporting the previous allocation to P. devosi, although substantial overlap with Chinese fossils could also indicate close affinities with P. weidenreichi. The hypothesis that both species represent one chronospecies cannot be ruled out. Two fossil specimens, one from Tam Hay Marklot (Laos, Late Pleistocene), and another from Sangiran (Java, Early to Middle Pleistocene), along with some specimens within the Punung sample (Java), exhibit affinities with Pongo abelii. The Punung fossils might represent a mix of early Late Pleistocene and later specimens (terminal Pleistocene to Holocene) related to modern Pongo. The taxonomy and phylogeny of the complete Punung sample needs to be further investigated.

Dataset Information

Multi-protease analysis of Pleistocene bone proteomes

Publications

Multi-protease analysis of Pleistocene bone proteomes.

Similar Datasets

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