Project description:Here, we sample small proteomes from the interior enamel of 10 fossils deposited at seven paleontological sites between 1.5 and 29 Ma in the Turkana Basin, a region of northern Kenya in the East African Rift System. We find enamel protein fragments in all fossil specimens including a 29 Ma Arsinoitherium from Topernawi, belonging to a now extinct mammalian order. Identified proteins include the classical structural enamel proteins amelogenin, enamelin, and ameloblastin, but also uncommon enamel proteins including collagens and proteases. Protein fragment abundance and average length decline in progressively older fossils, but we observe significant variability in Early Miocene preservation from site to site, with proboscidean fossils from 16 Ma Buluk preserving substantially more proteins than Rhinocerotidae and Anthracotheriidae fossils from the marginally older Locherangan (18 Ma) and Hippopotamidae from the younger site of Napudet (c. 5-11 Ma). Most specimens yield known clade-specific diagenetiforms that support field taxonomic identifications, with the notable exception of the Arsinoitherium that is without living relatives. Consensus phylogenetic trees suggest the potential for paleoproteomics in supporting taxonomic identifications and resolving evolutionary relationships of extinct taxa but should be approached with caution due to sometimes sparse fragment identification and the potential for sequence diagenesis. We identify numerous likely modifications that support the ancient age of these proteins, and the oldest examples of advanced glycation end-products and carbamylation yet known. The persistence of protein sequences within dense enamel tissues in one of the persistently warmest places on Earth promises the discovery of far older proteomes that will aid in the study of the biology and evolutionary relationships of extinct taxa.
Project description:The tooth enamel proteome is enzymatically broken down during development, which leads to a heterogenous distribution of remaining peptides of a protein sequence in a grown individual's enamelome. After death of the organism, the heterogeneous distribution of remaining peptides may be enhanced, as the proteome further degrades. The pattern of this degradation is poorly understood, but it might happen at different rates depending on the site within the protein sequence, due to different chemical properties of the peptides and their interaction with the environment. To learn more about this process, we recovered six ancient enamel proteomes from Equidae and Proboscidea fossils from Spain. The fossils span an age range of <100 ka to 11.6 Ma.
Project description:The ability to sequence genomes has far outstripped approaches for deciphering the information they encode. Here we present a suite of techniques, based on ribosome profiling (the deep-sequencing of ribosome-protected mRNA fragments), to provide genome-wide maps of protein synthesis as well as a pulse-chase strategy for determining rates of translation elongation. We exploit the propensity of harringtonine to cause ribosomes to accumulate at sites of translation initiation together with a machine learning algorithm to define protein products systematically. Analysis of translation in mouse embryonic stem cells reveals thousands of strong pause sites and novel translation products. These include amino-terminal extensions and truncations and upstream open reading frames with regulatory potential, initiated at both AUG and non-AUG codons, whose translation changes after differentiation. We also define a new class of short, polycistronic ribosome-associated coding RNAs (sprcRNAs) that encode small proteins. Our studies reveal an unanticipated complexity to mammalian proteomes.