Proteomic and lipidomic analysis of mammoth bone by high-resolution tandem mass spectrometry coupled with liquid chromatography

Abstract

Investigation of archeological and paleontological artifacts at the molecular level has become a trend over the recent years. Paleogenomics provides information about the evolution of ancient species; paleoproteomics was recently established as branch of conventional proteomics dedicated to the study of proteomes of extinct organisms. At the same time paleolipidomics, which could focus on the investigation of lipids of ancient species, is not developed yet, though the investigation of fossil lipids may have potential to provide information about past diseases or diet. Here we present the investigation of an ancient fossil bone of a Siberian mammoth using combined proteomics and lipidomics approaches based on high-resolution tandem mass spectrometry coupled with liquid chromatography (LC-MS/MS). Using various experimental approaches, we have reliably identified 98 proteins and 73 lipids in three tissue regions of the mammoth bone. We have also compared the proteome profile of ancient mammoth bone with those of a modern elephant.

Exceptionally preserved extracellular bone matrix proteins from the late Neogene proboscidean Anancus (Mammalia: Proboscidea)

“…In gel electrophoresis, Tuross (1989) detected three different protein bands, for one band she supposed the presence of albumin because of the similar molecular weight. Other related investigations on Pleistocene mammals were published recently (e.g., Cappellini et al 2012;Hill et al 2015;Kostyukevich et al 2018).…”

“…Particularly Schweitzer and her group (Schweitzer et al 2013), who was very active and successful during the last 15 years, sequenced protein fragments from bone collagen of a 100,000 to 600,000-year-old mastodon and a 68-millionyear-old dinosaur (Asara et al 2007). However, also other groups identified non-collagenous ECM proteins such as osteonectin and osteopontin in 120 ky Pleistocene mammals using mass spectrometry (Cappellini et al 2012;Hill et al 2015;Kostyukevich et al 2018), while Kostyukevich and colleagues also detected with coupled liquid chromatography lipids (Kostyukevich et al 2018). Also impressive is the work of Cappellini and his group dealing with tandem mass spectrometry which enables the sequencing of collagen type 1 from a 1.5-million-year-old sample of a tooth from Cretaceous fossil remains (Cappellini et al 2019).…”

A Chemical Framework for the Preservation of Fossil Vertebrate Cells and Soft Tissues

“…Lipids also undergo NonP taphonomic alteration processes. For example, fatty acids are rapidly hydrolyzed from the glycerol unit in phospholipid and glyceride diagenesis (Briggs et al 2000;Kostyukevich et al 2018;Nolan et al 2020); the resultant fatty acids can then be hydroxylated or methylated, among other NonP taphonomic alterations (Stefanova & Disnar 2000). While NonP taphonomically altered lipids and sterols often serve as biomarkers within sedimentary organic matter (Briggs & Summons 2014;Mackenzie et al 1982;Mackenzie et al 1981;O'Reilly et al 2017;Philp & Gilbert 1987), such biomarkers have not often been reported within vertebrates prior to the Neogene (Briggs et al 2000;O'Reilly et al 2017).…”

“…Unaltered phospholipids and glycerides are rapidly hydrolyzed post-mortem, releasing their constituent fatty acids from glycerol (Briggs et al 2000;Kreps et al 1981;Schoenen & Schoenen 2013). Intact phospholipids are generally not recovered even from permafrost frozen Pleistocene soft tissues (Kostyukevich et al 2018;Kreps et al 1981). Unbound, saturated fatty acids, on the other hand, can be recovered from permafrost specimens (Kostyukevich et al 2018;Kreps et al 1981).…”

“…Intact phospholipids are generally not recovered even from permafrost frozen Pleistocene soft tissues (Kostyukevich et al 2018;Kreps et al 1981). Unbound, saturated fatty acids, on the other hand, can be recovered from permafrost specimens (Kostyukevich et al 2018;Kreps et al 1981). Volatile, unbound fatty acids have even been reported from whole bone extracts of Pliocene, Miocene, and Oligocene specimens (Shinmura & Sawada 2010;Thiel et al 2014;You-Xing et al 2007).…”