ANCIENT PROTEINS nestled in fossils contain troves of information about long-dead creatures. However, like all ancient molecules, proteins degrade. Until recently the oldest proteins recovered for reliable, in-depth analysis were around 4m years old. But two separate studies published in Nature on July 9th, one by researchers at Harvard University and the Smithsonian Institution and another led by researchers at the University of Copenhagen, have recovered ancient proteins, some of which could be up to 29m years old. The discoveries should help palaeontologists investigate the behaviour, diet and evolution of animals long thought too old to be studied with molecular tools.
PREMIUM I gotta get my protein(Photograph: Martin Lipman)
Both research teams recovered the ancient proteins from tooth enamel, the hardest substance in vertebrates’ bodies, in fossils they assessed to be many millions of years old. They first ground the enamel to a powder and then applied a chemical solution to draw out the proteins. To confirm that the proteins were not the result of modern contamination, they identified chemical damage to the proteins accrued over time, a process called diagenesis. The amount of damage lined up with what they would expect for fossils of that age.
The team from Harvard and the Smithsonian Institution focused on the enamel of big African animals, such as elephants, in Kenya’s Turkana Basin, which were between 1.5m and 29m years old (although they have high confidence only in fossils up to the age of 18m). Finding old proteins in one of the warmest places on Earth, where biological molecules easily break down, suggested that even older proteins could be recovered in better conditions. The researchers from Copenhagen confirmed this suspicion. In the Haughton Crater in the much colder climes of the Canadian Arctic, they managed to extract protein sequences from the tooth of a 24m-year-old rhinocerotid, a squat, single-horned mammal in the rhinoceros family.
Having recovered the proteins, the two teams were able to compare their sequen-ces against databases of known protein sequences from other species. This allowed them to place the extinct species on the tree of life. For example, the Harvard study suggests that an 18m-year-old creature in the Anthracotheriidae family is probably the ancestor of modern hippos, whereas the close relatives of a rhino-like animal called Arsinoitherium, thought to be 29m years old, are all extinct.
Enrico Cappellini, who was part of the Copenhagen study, says that the new discoveries expand the timeline of proteins available for analysis ten-fold compared with ancient DNA (aDNA), which lasts about 1m years. That means palaeontologists can now understand the evolution of organisms that are too old for other ancient molecular analysis. Future analyses of carbon and nitrogen isotopes within the preserved proteins could also offer insights into the diet, environment and migratory behaviour of extinct species.
There are tantalising hints that scientists may have even older proteins to discover. Back in 2009, researchers from North Carolina State University retrieved fragments of collagen protein from the fossil of an 80m-year-old duck-billed dinosaur called Brachylophosaurus canadensis. Although the collagen had degraded into small bits, they were able to confirm that it was of a specific kind now only found in birds. Better preserved proteins yet to be found might be able to reveal even more.
Commenting on the Copenhagen findings, Matthew Collins, a palaeoproteomics expert at the University of Cambridge who was not part of either study, says the results are “spectacular if true” and that they could transform interpretation of fossil records. Because some proteins in tooth enamel vary between the sexes, they could help determine the sex of some fossils, which can otherwise be tricky. Placing species on the tree of life could also clear up long-running evolutionary disputes, such as the debate over the true ancestry of horses. Whereas aDNA took palaeontologists into the distant past, it seems ancient proteins could take them further still.
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