Protein preservation and DNA retrieval from ancient tissues

Area of Science:

• Paleogenomics
• Biogeochemistry
• Analytical Chemistry

Background:

• Ancient DNA (aDNA) retrieval from fossils is challenging and often debated.
• Substantiating aDNA claims requires evidence of other molecular preservation within the same fossil sample.
• Protein preservation quality is a key indicator for potential aDNA recovery.

Purpose of the Study:

• To evaluate flash pyrolysis coupled with gas chromatography-mass spectrometry (GC-MS) as a method for assessing protein preservation in fossil remains.
• To correlate protein preservation quality with the success of ancient DNA recovery.
• To identify environmental factors influencing macromolecule preservation in fossils.

Main Methods:

• Flash pyrolysis coupled with GC-MS was employed to analyze protein degradation products in 11 archaeological and paleontological samples.
• Analysis focused on identifying and quantifying pyrolysis products, specifically 2,5-diketopiperazines derived from proline-containing dipeptides.
• Samples included specimens with previously authenticated aDNA sequences and those that yielded no meaningful DNA.

Main Results:

• Abundant 2,5-diketopiperazine products were detected in samples, including the Neanderthal-type specimen.
• The relative abundance of these peptide hydrolysis products served as a reliable index for DNA preservation potential.
• Four of the analyzed samples originated from arctic/subarctic regions, highlighting the role of low temperatures in macromolecule preservation.

Conclusions:

• Flash pyrolysis-GC-MS is a rapid and effective technique for predicting the potential for ancient DNA preservation in fossil materials.
• Protein degradation patterns, particularly the presence of specific diketopiperazines, offer valuable insights into DNA survival.
• Optimal preservation of macromolecules, including DNA, is associated with cooler environmental conditions.