Proteins From The Ancient Past

Scientists have identified 126 proteins in a 43,000-year-old woolly mammoth femur (J. Proteome Res., DOI:10.1021/pr200721u). Although proteins have been found in ancient bones before, this is the first time that such a wide variety has been detected.

The work “is the first description of a substantive component of an ancient proteome,” says Peggy H. Ostrom, an expert on ancient bone proteins in the zoology department at Michigan State University. This “landmark study,” she says, “launches the field of paleoproteomics into a new realm.” It could lead to a better understanding of how organisms are related evolutionarily.

Enrico Cappellini of the Center for GeoGenetics at the Natural History Museum of Denmark, Jesper V. Olsen of the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen, and coworkers used high-sensitivity, high-resolution tandem mass spectrometry to sequence proteins extracted from a woolly mammoth bone that had been preserved in Siberian permafrost. Their rich harvest of ancient proteins may be due to two factors: The deep freeze protected the proteins from degradation, and the researchers’ methods are sensitive enough to capture previously undetected ancient proteins from bones found in temperate climates.

In previous work, researchers saw only the most abundant bone proteins—collagen, osteocalcin, and a handful of others—Cappellini says. The current work found a much wider range of protein types. Most surprising and potentially worthwhile was the amount of albumin the researchers were able to detect, Cappellini says. The variability of albumin among species relative to other proteins makes albumin a good candidate for providing evolutionary information not possible with other proteins.

“This is very exciting work, because it is the first to indicate the recovery of a significant proportion of noncollagenous proteins in fossil bone,” says Mary H. Schweitzer of North Carolina State University and the North Carolina Museum of Natural Sciences. “This study holds hope for rigorous molecular testing of phylogenetic hypotheses using biomolecules other than DNA. In general, proteins are thought to be more abundant and some proteins more resistant to degradation than DNA.”

Researchers have long hoped that analytical technology would become sensitive enough that ancient proteins could not only be detected but could also be sequenced, notes Hendrik Poinar, an expert on sequencing of ancient DNA at McMaster University in Hamilton, Ontario. “The real hope is that in samples where the DNA no longer survives, the proteins may still persist, allowing us to harness sequence information into deep time,” he says.

Cappellini hopes to extend the analysis to even older samples. “What happens if we move back 100,000 years?” he asks. “Will we be able to identify the same set of proteins?” That’s something he hopes to find out.