Biominerals can harbour intact peptide sequences over geological timescales
Probing ancient egg shells for informations about the past
There are several ways how scientists can look back into the past. Digging deep wholes into glacial ice of Greenland or Antarctica allowed climate researchers to gain insights into past atmospheric compositions. Similiar to how you can count the rings on a tree, counting layers of ices is straightforward and reliable and can go back hundreds of thousands of years.
Then there is carbon dating, which is a bit more complicated, as it uses the radioactive decay of the Carbon-14 isotope once ingested and bound by the leftovers of dead animals. Its accuracy is amazing, however the range is only about 50.000 years back and not further.
If scientists wanted to look back even further, they would rely on other radiometric methods, for example meassuring rare isotopes in rock layers to identify the age of fossils from dinosaurs to ancient cetaceans.
The problem here is that radioactive elements are common only in rocks with a volcanic origin, and so the only fossil-bearing rocks that can be dated radiometrically are a few volcanic ash layers.
Now unfortunately, reconstructing evolutionary pathways by comparing dated fossils that happen to be hit and burried by vulcanic ash layers has been a puzzle with many missing pieces. That is why, even today, there are many “gaps” from one fossil ancestor to another, and anytime one of these puzzle pieces gets discovered, it’s big news, like here or here.
One big problem scientists always face with fossils is the “morphological” similarity; basically they can only really compare how similar fossils look to each other. But we all know that looks are not everything.
With the beginning of the genome era, there has been tremendous progress in another method to reconstruct evolutionary history: The sequencing of ancient DNA. DNA is a long chain-like molecule built up of different sugars that contain our genomic information; the blueprint of life.
If stored dry and cool, DNA is a remarkable stable molecule that can withstand the test of time for quite long. In 2013, researchers could extract 700.000 year old DNA from an ancient Pleistocene horse. The cool part about DNA sequencing is the richness of information it can bring forth.
Ancient DNA sequencing allows us to look not only “morphologically” at any given species history; it provides a molecular record of how the “blueprint” changed overtime.
Naturally, this field of research is a goldmine of knowledge for any biologist, as well as source of moonshot biology experiments like George Church’s efforts to bring the Mammoth back to life.
However, ancient DNA has been rare and hard to find. Furthermore, when we talk about geological timescales, DNA is really not that useful by going back only hundreds of thousands of years.
In a recent paper in the scientific journal Elife, researchers from all over the world (UK, US, Spain, Denmark, Israel, Tanzania, South Africa) came together and reported a new method of probing the past: Peptides bound in Biominerals.
Biominerals are chemical compounds produced by living organisms, such as silicates in algae, or shells and bones, basically anything that can withstand organic degradation.
They found that peptides or proteins, which consist of amino acids, can hitchhike on or within biominerals to be preserved throughout the ages.
Usually, DNA as a molecule would be way more stable than any protein, as proteins are subjected to unfolding (=lose compact 3D structure) and subsequent hydrolysis (=degradation). However, by probing ancient egg shells of ostriches, the study led by Demarchi et al. could show that the binding to biominerals can be extremely beneficial for the longevity of proteins over geological time scales. Part of this longevity comes from the preservation of the protein’s 3D structure upon binding to mineral surfaces, as well as to “locking” of water molecules in place on those surfaces.
Imagine the biominerals as some kind of bodyguard that keeps other molecules away from their protected protein, as well as keeping everything around the protein kind of calm and stable.
In their experiments, Demachi et. al. used a computer simulation method called “molecular dynamics”, where they calculated that the protein sequences that are able to survive the longest are stabilized by strong binding to the surface of the mineral crystals. However to verify the authenticity of their results, the researchers needed to use a combination of several approaches, from electron microscopy to mass spectrometry, which they recommend using as a standard for ancient protein studies for the future.
In this study, we also set out parameters for the authentication of ancient sequences: the combination of the consistency in patterns of protein degradation and survival of particular peptide regions, independent replication of the results and an in-depth analysis of analytical blanks provide overwhelming evidence for the endogeneity and integrity of the peptides recovered. We suggest that all ancient proteomics studies undertake a similar approach to verify the authenticity of the sequences reported.
One important sidenote: Protein sequences are not completely equivalent to DNA sequences, as they cover a slightly narrower information density. Nevertheless, protein sequences are still very information rich and can be mapped back to the genomic information to a certain extend.
In summary, this study could show that by dating those ancient biomineral-bound peptides, we can look further back into our evolutionary past than ever before. While with DNA, we are limited to a few hundred thousand years, peptides found in this form will allow us to probe the evolutionary path of complex life tens of millions of years ago. What amazing things we will find there is yet to be seen.
Palaeontologists and palaeoanthropologists, get ready to discover!
This story is part of advances in biological sciences, a science communication plattform that aims to explain ground-breaking science in the field of biology, medicine, biotechnology, neuroscience and genetics to literally everyone. Scientific understanding has too many barriers, let’s break them down!
