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Protein sequence comparison of human and non-human primate tooth proteomes

ABSTRACT: In the context of human evolution, the study of proteins may overcome the limitation of the high degradation of ancient DNA over time for providing biomolecular information useful to precise the phylogeny of hominid taxa. Here, we have analysed and compared the tooth proteome of five extant primates (human, gorilla, chimpanzee, orangutan and baboon) using a shotgun proteomics approach. Twenty five proteins were shared by the five datasets, and may be considered as the most representative tooth proteins with a chance of being retrieved from older samples. Some of them were identified by peptides specific to the species, thus allowing to draw up a combinatory panel of peptides with species signature that could be helpful for the taxonomic characterization of ancient samples

INSTRUMENT(S): Orbitrap Fusion ETD

ORGANISM(S): Papio Hamadryas Homo Sapiens (human) Gorilla Gorilla Gorilla Pan Troglodytes (chimpanzee) Pongo Abelii

TISSUE(S): Tooth

SUBMITTER: Emmanuelle Mouton Barbosa

LAB HEAD: Catherine Mollereai

PROVIDER: PXD018933 | Pride | 2020-11-17

REPOSITORIES: Pride

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			Action	DRS
	OFCCF180606_03_SP01_CCF01519_BLK1_TR1_AllSpecies.msf	Msf
	OFCCF180606_03_SP01_CCF01519_BLK1_TR1_AllSpecies.raw	Raw
	OFCCF180606_04_SP01_CCF01519_BLK1_TR2_AllSpecies.msf	Msf
	OFCCF180606_04_SP01_CCF01519_BLK1_TR2_AllSpecies.raw	Raw
	OFCCF180606_08_SP01_CCF01520_T1_TR1_Gorilla.msf	Msf

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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.

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Protein sequence comparison of human and non-human primate tooth proteomes

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