SciBar at The Vat & Fiddle - Biomolecules in The Fossil Record: Sequencing Proteins in Amber

Palaeontology is the study of ancient life. The way that we do this is by studying the fossil record, although we're more interested in what these animals were like when they were alive. By comparing the fossils to creatures alive today, we can learn more about them and how they lived. However, we have different datasets in the fossils compared to living organisms. All we have for the fossils is their morphology (how they looked) we don't have any biomolecules. So, it's important that we find these so that we can compare them with modern organisms.

By looking at their proteins, we can hope to better understand dinosaurs. Their closest living relatives are birds. In fact, birds ARE dinosaurs but there is nothing around that is similar to T-Rex or Triceratops. Even something like a crocodile isn't really a great analogue as it's nowhere near the same size. If we can examine the protein, then the morphology of the creatures is less important.

Proteins are valuable tools for studying living organisms and they preserve better than DNA. We have only just discovered the technique for sequencing proteins but we can now read off the amino acids one by one. Everything you can do with DNA, you can do with protein – you can even identify an individual by their protein. In proteins, you are getting the actual functional unit, if we can find them then they would be incredibly useful in fossils. One drawback that protein does have over DNA is that you can't use protein to clone a dinosaur.

How do we find fossil biomolecules? We have to do a chemical analysis. What fossils are most likely to contain intact proteins? We need something very well preserved so we have to consider how proteins break down and what conditions allow the proteins to survive. Water chemically reacts with protein and breaks it down. Three things inhibit this:

1) Cold temperatures
2) Binding to mineral surfaces
3) Dehydration

The first two of these extend protein preservation to around 4 million years. For example, camel bones found in the arctic were around 3.5 million years old (cold temperature) and ostrich eggshells were found in Africa that were around 3.8 million years old (binding to mineral surfaces) By comparison, DNA only lasts around 100,000 years, even in cold temperatures.

Amber dehydrates enclosed tissues, which should enhance soft tissue preservation of proteins. Dinosaurs and proteins overlap in fossils in amber. The soft tissue is preserved so maybe the biomolecules are too. There are preserved dinosaur parts in amber, specifically feathers. Now, feathers are made entirely of protein so the question is, do proteins preserve in fossil feathers in amber?

However, to sequence the protein you have to destroy the fossil and fossilised feathers are extremely rare. Hence, the museums that own these samples are very reluctant to allow their amber to be tested. To prove that the concept works, Victoria had to do some experimental investigations using chicken feathers. It's difficult to simulate the passage of 65 million years in the lab but by heating to between 110^oC and 140^oC for three weeks, the protein degrades in the same way. This also turned the resin into amber.

Amino acids have right hand and left hand forms. When they are bonded into a protein they are all left handed. When the protein breaks down, the amino acid becomes free and can become right handed. So, by measuring the right handedness, we can tell how degraded the protein is. Experiments have shown that protein could last up to 400 million years in amber.

Sequencing these proteins could answer a lot of palaeontological questions. It would also confirm whether the feathers come from dinosaurs or from birds as we can't tell from age or appearance - the only other easy way to tell is if they are attached to a piece of dinosaur. We can then hope to understand the evolution of feathers and hence the evolution of flight. We may be able to move onto other things that are preserved in amber, such as spider webs, which are 100% protein. This would help us understand the evolution of spiders and how ancient spider webs worked.

Once you take a 3D image of a fossil in amber, it can tell us nothing more about the morphology.  That's not to disparage the morphology, we can learn about things like muscles and teeth, which tell us whether an animal is a carnivore. Trace fossils can things like footprints and proof of digging. However, proteins could tell us about how dinosaur feathers worked - where they for waterproofing, flying, just for show to attract mates or maybe for warmth? The fact that dinosaurs had feathers and feathers are so good at insulating could actually show that dinosaurs were warm blooded.

The longer the protein fragment, the more we can tell from it. The nearest thing to feathers is the keratin in scales but this is in shorter chains and is a much simpler protein than that in feathers. Obviously, modern bird feathers are the nearest modern structure to dinosaur feathers and there is now a scheme in place to map all of the protein from modern birds. Once that database is complete, there will be a lot of records to compare the dinosaur feather protein to.

Birds first evolved from theropods in the Jurassic period. The feathers in amber are from the Crustaceous period, far later. So, we can't tell exactly how dinosaurs evolved into birds. However, we do know that it wasn't the bid-hipped dinosaurs that evolved into birds, rather it was the lizard-hipped ones.

SciBar returns to The Vat & Fiddle on Wednesday 29 March, 7:30pm.

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