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Environment and sustainability

Ancient proteins are the new hot property in science

The past does not simply hold details about our history. Knowledge on human evolution can also provide important information that can be used to combat the development of disease now. The use of prehistoric DNA has revolutionized evolutionary research and archaeology in the past 30 years. Unfortunately, ancient DNA is not always well preserved. A new study of relationships between sloths has been published in one of the world’s most prestigious journals – not because of the sloths but more because its analysis of prehistoric proteins will revolutionize science.

A new technology enables researchers to step further back in time by a factor of up to 10-fold because proteins remain intact that much longer than DNA. Excavations of prehistoric sites are therefore much more likely to find intact protein than DNA. The great technical advances in mass spectrometry enable researchers to decode sequences from proteins that are millions of years old, and this has already solved prehistoric mysteries.

“Our latest study of the early evolution of sloths shows the potential of the new technology. Biologists can spend decades assessing kinship based on bone size, structure and shape, but we can determine the kinship in hours or days based on a very few protein samples. We even discovered that the morphological conclusions were wrong. So this technology enables us to answer questions that DNA has been unable to solve,” says a co-author, Matthew Collins, Danish National Research Foundation Niels Bohr Professor, Evogenomics Group, Globe Institute, University of Copenhagen and McDonald Chair, Institute of Archaeological Research, University of Cambridge, United Kingdom.

Powerful method

Today, only two types of the Folivora suborder of sloths still exist, but back in the Cenozoic Era 1.8 million years ago, sloths were widespread in many parts of the Western Hemisphere. However, because many of these animals lived in humid and hot areas, which have an unfavourable climate for preserving DNA, researchers have not been able to identify the relationships between the types of sloths using current methods.

”We managed to obtain 120 samples from 24 species. Of these, we found enough protein for analysis from about one third. We then used mass spectrometry to determine the sequence of the same protein, collagen, in each sample. Then we could start the process of examining the kinship relationships of the sloths based on the sequences.”

The researchers were then surprised to discover that the two-toed sloth of the Choloepus genus and the three-toed sloth of the Bradypus genus originated from two different families of the Folivora sloth suborder: Choloepus from the Mylodontidae family and Bradypus from the Megatheriidae family.

“Previous morphological studies suggested that Choloepus and Bradypus were more closely related. This new method provides a more accurate picture than is possible from morphological studies alone. The protein sequences are not as rich as DNA, and are more prone to homology. In a way, it is like unearthing extra skeletal elements with new bits of evidence .”

Evolution mitigates catastrophic effects

Although the new method has many possible new applications, it works best together with DNA analysis. Protein analysis can detect intact proteins in more places and further back in time, but DNA analysis provides more information.

“DNA analysis provides both sequences that encode proteins and sequences that are never translated into proteins. The DNA code may also change without this changing the protein encoded by the DNA. This is because several three-letter codon combinations in the DNA code get translated into the same amino acid in the final protein.”

For example, the codons GGT, GGC, GGA and GGG are all translated into the amino acid glycine. So, although the DNA code may change, the protein may not.

“Evolution also tends to mitigate the effects of some of these mutations in the DNA that arise through natural evolutionary changes, often because mutations in the equivalent proteins would have catastrophic effects on the organism.”

Enormous potential

The proteins thus change much less than DNA, but prehistoric proteins also contain much less information than prehistoric DNA.

“Nevertheless, combining protein and DNA techniques works very well. DNA technology is very accurate, but we can find protein in many more locations, which provides greater depth in the analysis.”

According to Matthew Collins, protein analysis has far greater development potential for new lines of investigation in archaeology and heritage science than the more mature field of DNA sequencing because most objects made of biological material have proteins.

”We are only now realizing how great the potential is as we discover how far back in time proteins have survived, where we find them and especially how much information we can extract from them. In addition, we can investigate more than our prehistory. This knowledge can also be used in the present era, such as in investigating ageing.”

Palaeoproteomics resolves sloth relationships” has been published in Nature Ecology & Evolution. Co-author Jesper Velgaard Olsen is Deputy Center Director and Professor, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen.

Matthew James Collins
Professor
I conduct research on the persistence of proteins in ancient samples, using modelling to explore the racemization of amino acids and thermal history to predict the survival of DNA and other molecules. Using a combination of approaches (including immunology and protein mass spectrometry) my research detects and interprets protein remnants in archaeological and fossil remains.