Scientists discover ancient protein and DNA sequences in same fossil

For the first time in the world, researchers at the University of Newcastle upon Tyne, UK, along with collaborators at the University of Oxford, Harvard University, and Michigan State University have uncovered two genetically informative molecules from a single fossil bone. In addition to the recovery of mitochondrial DNA, the complete sequencing of a bone protein, osteocalcin, makes this a major scientific breakthrough. Extending this work to additional fossils could change perceptions of evolutionary theory. Results of the study are published in the December issue of GEOLOGY, published by the Geological Society of America.

Christina Nielsen-Marsh of the University of Newcastle upon Tyne, along with colleagues at the University of Oxford, Harvard University, and Michigan State University, examined the molecular structure of two fossilized Bison priscus bones, one from Siberia and the other from Alaska. The bones are more than 55,000 years old, although their age is somewhat imprecise because they are beyond the limits of radiocarbon dating. The Siberian fossil ultimately revealed both mitochondrial DNA and a complete sequence of osteocalcin, a protein found in all bones that is involved in bone formation.

The researchers demonstrate, using immunological data, that osteocalcin remains in bones heated to high temperatures (165oC) for several hours and is measurable in bones that are around 120,000 years old, emphasising the survivability of the protein. According to Nielsen-Marsh, “The research has the potential to be applied to much older fossils and extend our knowledge about the genetic make-up of ancient species further back into geological time.” The team is hoping that in the future their approach may be able to find the answers to long-standing evolutionary puzzles.

Protein sequencing was carried out at Michigan State University, using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). Important steps in the development of this technique are credited to this year’s Nobel Prize (Chemistry) winning scientist Koichi Tanaka. Using a variety of approaches, the osteocalcin from the ancient bison bone was fragmented and the information used to construct the amino acid sequence.

Remarkably, the primary sequence of the protein was recovered intact, including the relatively unstable carboxylated glutamic acid (gamma-carboxy glutamic acid) residues. As a consequence of this study, the team has a new optimism regarding the potential for protein sequencing and extending molecular records farther back in time.

Protein sequences can be directly related to the genetic code of DNA. The sequence of amino acids (the building blocks of proteins) record genetic information transferred from DNA. According to Nielsen-Marsh this is important because mutations in DNA over long periods of time result in changes in proteins that contribute to the evolution of life. Calculations suggest, however, that DNA may only survive for up to 100,000 years, whereas proteins may survive for up to10 million.

The traditional way of comparing ancient and modern species to determine how they have changed over time is morphology, where bones are compared for shape and size. This may involve a large margin of error, however, as it can be subjective and bones such as skulls are malleable and prone to changing shape.

According to Nielsen-Marsh, “By extracting biochemical information from fossils, scientists utilize tools that avoid these difficulties and offer more objective comparisons between ancient and modern species.” This approach could possibly unearth new knowledge about evolutionary relationships.

“This research is groundbreaking,” continues Nielsen-Marsh, “because it finally puts to rest the question of whether indigenous proteins can exist in fossil bones beyond radiocarbon dating age. Moreover, intriguing data from our laboratories suggest that extending protein sequencing well beyond 55,000 years is a realistic possibility.”

Funding for the study was provided by the Wellcome Trust and the National Science Foundation.

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