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Biotechnology peers into fossils’ past


British and American geoscientists using molecular biology techniques have succeeded in identifying the world’s first complete protein sequence from fossils: two bison bones, both more than 55,000 years old, recovered from permafrost in Alaska and Siberia. The find also included mitochondrial DNA from the Siberian bison bone. The discovery is being heralded as a breakthrough, providing a new method that evolutionary scientists can apply to their fossil studies. Protein evidence and DNA from ancient bones may also help in better understanding human evolution.

“We’re entering the paleogenomic era,” says Hendrik Poinar of the Max Plank Institute for Evolutionary Anthropology in Leipzig, Germany. With this rise in genomic research of the past has emerged a target field of study on proteins. He credited the push for paleontologists to enter proteomics, the study of proteins, to Mathew Collins of the University of Newcastle upon Tyne in the United Kingdom. Collins is one of seven authors of the bison bone report published in last month’s Geology. Lead author of the report, Christina Nielsen-Marsh, also of Newcastle upon Tyne, explained that proteins, unlike DNA, have the potential of lasting in mineralized bone material for perhaps tens or hundreds of millions of years.

Christina Nielsen-Marsh weighs small quantities of bone powder (about 20 milligrams) from a Siberian bison fossil. From these samples her team recovered protein osteocalcin and DNA sequences. Courtesy of C. Nielsen-Marsh.

Previous methods to sequence protein from fossils, however, failed to result in a complete sequence and most ancient DNA studies have examined only the last 50,000 years. This is the first paper to report both DNA and a complete protein sequence preserved together in a sample that was radiocarbon dated to be at least 55,600 years old. The discovery of both in such an old bone, along with the complete protein sequence in the other bone, dated to be at least 58,900 years old, indicates that protein can play an important role in providing a molecular record of the ancient past when DNA may no longer be available to study. Just how far back the DNA or protein records might go is anyone’s guess.

The specific protein sequenced, osteocalcin, is exclusively found in vertebrate animals and takes part in bone formation by binding strongly to the bone mineral. The team applied a familiar method among molecular geneticists to fossil bison and discovered they could derive the complete sequence of osteocalcin from small amounts (20 milligrams) of crushed bone. Previous efforts to extract protein sequences required large quantities of the sample material, resulted in only parts of the protein being sequenced and left ambiguity as to whether the amino acids that made up the protein included contaminants from the fossil environment.

Neilsen-Marsh’s team sequenced the osteocalcin using matrix-assisted laser desorption ionization mass spectrometry — a technique that Koichi Tanaka of Shimadzu Corp. in Kyoto, Japan, helped pioneer in 1988 and for his efforts received part of the 2002 Nobel Prize in Chemistry. Rather than using a reagent that reacts with amino acids one-by-one to determine their order in a protein, the laser desorption method relies on a laser to blast apart the sample and release the protein molecules intact.

The team found evidence indicating a match between the ancient bison protein sequence and modern bison. They also confirmed an expected difference between the bison and cow sequences, the result of a single amino-acid substitution. Where DNA can tell the difference between individuals, protein can only say if the two samples are the same species or not. In that sense, “proteins act like a crude molecular clock,” Nielsen-Marsh says. Combining the fossil record with modern taxonomy allows scientists to estimate when species diverged; applying a protein test to a fossil could theoretically now examine those estimates.

Still, finding fossils that will reliably provide clear results will depend on the conditions that preserved them. “The key is temperature,” Nielsen-Marsh adds. The hotter the environments the faster the biological samples degrade. DNA held at around 0 degrees Celsius can last for an expected 100,000 to 120,000 years, she says. Whereas protein, she adds, could last a thousand times as long at that temperature, going back perhaps 110 million years. “But it is highly unlikely that we’re going to find fossils covered in ice since then because it is long before the last ice age.” So she suggests looking for younger fossils in warmer climes, giving an ideal fossil candidate a more realistic 1-million-year-old age. That puts the ball in the human evolution court.

“What this means for humans and Neanderthals is fantastic,” Poinar says. He recommends building a new center of research dedicated to the field of paleogenomics. “Then we’ll see with lightning speed technological changes and the possibility to go back and sequence Neanderthal proteins. Interested in speech gene products? We could explore bones to determine if Neanderthals were speaking or not.”

A problem he foresees, however, is the current state of fossil, bone and even seed bank collections. “We’re entering a dawn of a new era, but generations from now may not see it that way.” With biodiversity dwindling on a daily basis, museums will play a key resource for materials that might hold such molecular secrets intact. But current methods for displaying and collecting ancient and modern specimens often disregard molecular investigations.

“What’s the only difference between DNA of a Neanderthal and the exogenous DNA from the curator handling it?” Poinar asks.

Time.

“Right, age is the only difference and the only real way to separate them is to look at the isotopic signature within them.” But over time, oxidation can damage DNA making it difficult to extract longer or complete sequences. “In 20 years nobody is going to want to go to a museum and sequence in small 100 base-pair, overlapping sections. They will want to get 10,000 base-pair pieces sequenced, and nice, high-quality DNA will be out of the question,” Poinar says. Unless specimens are protected in antioxidating environments, researchers of the future will have to turn to protein sequencing out of necessity.

Christina Reed

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