Oldest mammalian proteome analyzed

Researchers have analyzed the oldest mammalian proteome yet. A team led by Frido Welker and Enrico Cappellini of the University of Copenhagen, Tomas Marques-Bonet of Pompeu Fabra University, and Wei Wang of Shandong University analyzed the enamel proteome of a Gigantopithecus blacki molar found in Chuifeng Cave in south China, a site dating to approximately 1.9 million years ago (Nature 2019, DOI: 10.1038/s41586-019-1728-8). The choice of acid to use for demineralization affected how many of the extinct primate’s peptide sequences the researchers were able to acquire. They recovered 127 more peptides when they used trifluoroacetic acid for demineralization than when they used hydrochloric acid. They recovered a total of 409 unique peptides from 6 proteins. Short peptide lengths indicate that the proteome was highly degraded. The evolutionary relationship of G. blacki to other ape species has been unclear. The new proteomic data allowed the researchers to make connections on the evolutionary tree. Their phylogenetic analysis suggests that G. blacki shares a common ancestor with the genus Pongo, which includes modern orangutans, and that Gigantopithecus diverged from Pongo about 10–12 million years ago. The researchers’ finding of a subtropical proteome suggests that recovering proteomes from even older specimens may be possible at higher latitudes, where less thermal degradation is likely.