In a landmark study,1 the Cappellini group performed a proteomic analysis of a 43,000-year-old femur belonging to a woolly mammoth (Mammuthus primigenius) that was preserved in Siberian permafrost and collected in Yakutia, Russia.2 This study represents the value of shotgun proteomics techniques in learning about ancient proteins and opens the door to potential phylogenetic inferences that were previously unavailable due to fossil degradation.
Remains from two mammoths (Dent mammoth, Mammuthus columbi, Colorado, and the La Sena mammoth, Mammuthus columbi, from southwest Nebraska) preserved in temperate climates were obtained and processed identically to the Siberian mammoth for comparison with the Siberian mammoth.
For this analysis, two microcore samples of approximately 2 mm in diameter were taken from the preserved mammoths. Proteins were extracted and analyzed using nanoﬂow reversed-phase C18 liquid chromatography along with tandem mass spectrometry (LC-MS/MS) as described previously,3 on an EASY-nLC system (Proxeon Biosystems) coupled to an LTQ-Orbitrap Velos (Thermo Scientific).
MS spectra obtained were searched using the Mascot 2.2 algorithm, in addition to 106,573 forward and reverse mammalian protein sequences and protein entries found in the Ensembl elephant (Loxodonta africana) genome.
Results of this study identified 126 proteins from the 43,000-year-old Siberian mammoth. More than 90% of the proteins reported had not been identified previously through high-resolution MS, and the proteomic profile observed was consistent with results described from modern bone by Jiang et al.4
Serum albumin was among the best characterized proteins. Albumin from the Siberian mammoth contained two single amino acid substitutions when compared with proteomes of extant African (Loxodonta africana) and Indian (Elephas maximus) elephants. Analysis also showed strong evidence of amino acid modifications due to postmortem hydrolytic and oxidative damage.
Nineteen and 35 mammoth bone proteins were also characterized from the two mammoth specimens of M. columbi found in temperate locations. The Cappellini group suggested that proteomics has the potential to provide protein and peptide data far beyond the cold, high-latitude environments. This study also represents the value of shotgun proteomics techniques in learning about ancient proteins and opens the door to potential phylogenetic inferences that were previously unavailable due to fossil degradation.
1. Cappellini, E., et al. (2012) ‘Proteomic analysis of a pleistocene mammoth femur reveals more than one hundred ancient bone proteins‘, Journal of Proteome Research, 11 (2), (pp. 917–926)
2. Römpler, H., et al. (2006) ‘Nuclear gene indicates coat-color polymorphism in mammoths‘, Science, 313 (5783), (p. 62)
3. Olsen, J.V., et al. (2009) ‘A dual pressure linear ion trap Orbitrap instrument with very high sequencing speed‘, Molecular and Cellular Proteomics, 8 (12), (pp. 2759–2769)
4. Jiang, X., et al. (2007) ‘Method development of efficient protein extraction in bone tissue for proteome analysis‘, Journal of Proteome Research, 6 (6), (pp. 2287–2294)