Ancient Proteins Found in Fossils up to 24 Million Years Old

Yomiuri Shimbun

6 days ago

WASHINGTON (Reuters) — Scientists in recent years have made progress in finding ancient DNA in fossils, gaining insight into organisms that lived long ago. But the oldest DNA obtained so far dates back about two million years. Proteins, a cell's molecular machinery, also offer valuable information and have the virtue of surviving much longer, as new research shows.
Scientists have now extracted and sequenced proteins from dental fossils of extinct rhinoceroses, elephants and hippopotamuses, including from a rhino tooth 21-24 million years old. Separate research teams found protein fragments in fossils from vastly different environments — the frigid High Arctic of Canada and a scorching rift valley in Kenya.
'Together, these complementary projects demonstrate that proteins — fundamental building blocks of living organisms that preserve information about evolutionary history — can be found in ancient fossils the world over,' said Harvard University evolutionary biologist Daniel Green, lead author of the Kenya fossils study published in the journal Nature.
This opens a new frontier for probing the deep evolutionary past, including the human lineage and perhaps even dinosaurs.
'Ancient proteins can tell us about an organism's evolutionary history by providing molecular data from specimens too old for DNA preservation. This allows researchers to clarify evolutionary relationships across the tree of life, even for species that went extinct millions of years ago,' said Ryan Sinclair Paterson, a postdoctoral researcher at the University of Copenhagen's Globe Institute and lead author of the Canada fossil study in Nature.
DNA and proteins are fragile and degrade over time, but proteins are more resilient. The oldest-known DNA is from organisms that lived in Greenland two million years ago. Until now, the oldest-known proteins preserved well enough to offer insight on evolutionary relationships were about four million years old, from the Canadian Arctic.
The new research pushes the boundaries of ancient protein research, a field called paleoproteomics, back by millions of years.
Proteins were obtained from teeth of five rhino, elephant and hippo species that lived 1.5–18 million years ago in Kenya's Turkana region. The proteins showed the ties between the ancient animals and their modern-day relatives.
Proteins also were extracted from a fragment of a tooth of an extinct rhino unearthed at a site called Haughton Crater in Nunavut, Canada's northernmost territory, that was up to 24 million years old. They showed how this species fit into the rhino family tree.
Haughton Crater's cold and dry conditions were considered ideal for preserving proteins. Preservation in the hot climate of Turkana was more unexpected.
DNA and proteins, fundamental molecules in biology, possess distinct structures and functions. Deoxyribonucleic acid is the blueprint for life, bearing instructions for an organism's development, growth and reproduction. Proteins perform numerous functions based on instructions from DNA.
'Proteins are encoded by our genetic code, DNA, so protein sequences reveal information about relatedness between different individuals, and biological sex, among other things,' Green said.
The scientists extracted peptides — chains of organic compounds called amino acids that combine to form proteins — found inside tooth enamel.
'Some proteins help build teeth, the hardest and most durable structures in animal bodies,' Green added.
'Enamel is mostly rock: a mineral called hydroxyapatite. But its formation is biologically mediated by proteins that guide both shape and hardness over time. Because these proteins become entombed deep within enamel mineral, we have some reason to expect that protein fragments can be preserved over many millions of years,' Green said.
Homo sapiens appeared about 300,000 years ago. Ancient proteins previously have been found in the teeth of some extinct species in the human evolutionary lineage, called hominins. The Turkana region has yielded important hominin fossils.
'Hominins have evolutionary origins and/or diversification in the area where our samples derive, so our results have promise in future exploration of the enamel proteome [set of proteins] of our evolutionary ancestors from the Turkana Basin of Kenya,' said study coauthor Timothy Cleland, a physical scientist at the Smithsonian Museum Conservation Institute in Maryland.
The proteins studied came from large-bodied species dating to the age of mammals that followed the demise of the dinosaurs that had dominated during the preceding Mesozoic era, which ended 66 million years ago.
Green said that in the new research the number of detectable proteins declined in progressively older fossils. But Green did not rule out finding proteins dating to the age of dinosaurs, saying, 'Newer and better methods for extracting and detecting ancient proteins could, perhaps, push paleoproteomics into the Mesozoic.'