Proteome degradation in fossils: investigating the longevity of protein survival in ancient bone

Abstract

RATIONALEWe report the use of proteomics techniques to study how the fossil bone proteome changes in complexity over one million years.METHODSWe include the attempted use of a previously unreported methodology in proteome research, to remove the dominant bone collagens using bacterial collagenase as well as conventional shotgun proteomics methodology following digestion with the protease trypsin. In this study we expand upon a set of 19 bovine sub-fossil specimens ranging over one and a half million years that had previously been shown to possess collagen, using a total of 46 LTQ-Orbitrap liquid chromatography/tandem mass spectrometry (LC/MS/MS) analyses containing 462,186 precursor ion analyses.RESULTSAlthough many types of proteins can typically be identified in recent bone, in degraded bone we observe a rapid loss of lower abundance proteins. Abundant serum proteins such as serum albumin and alpha-2-HS-glycoprotein appear to be more easily recovered in ancient bone, both being identified in specimens dating to the Early Pleistocene, the earliest period tested in this study. Proteins belonging to the leucine-rich repeat family such as lumican, biglycan and chondroadherin also survive well, possibly because of their interactions with bone collagen.CONCLUSIONSOf these 'survivor proteins' A2HSG shows a remarkable amount of sequence variation, making it potentially one of the most useful proteins to study for species identification and phylogenetic inference in archaeological and palaeontological bone.

Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne

“…Fourth, after exclusion of contaminants, protein composition was similar to other nonhominin bone palaeoproteomes (25,26). For these proteins, we observed the presence of additional diagenetic and in vivo posttranslational modifications (SI Appendix, Fig.…”

“…The identification of COL10α1 and additional proteins predicted to carry derived amino acid substitutions specific for Late Pleistocene clades within the genus Homo (34) in the data presented here and elsewhere for nonhominin palaeoproteomes (25,26) suggests ancient proteins are a viable approach to study the taxonomic affiliation of Pleistocene fossil hominins, in particular when ancient DNA is poorly or not preserved. So, the analysis of ancient proteins provides a second biomolecular method capable of differentiating between Late Pleistocene clades within our genus when adequate error-tolerant search algorithms are used.…”

“…This realization requires further investigation, as this has not been explored in-depth previously in the palaeoproteomic or the clinical literature (25,26). We hypothesize that COL10α1 or other cartilage-associated proteins could be retained in mineralized tissues that have reduced rates of remodeling (cranial sutures, epiphyseal plates), mineralized tissues that do not remodel (dentine), or bone regions that are in intimate contact with other tissue types (trabecular bone, articular surfaces).…”

“…GO annotation analysis further identified a significant group of blood microparticles (GO:00725262) such as albumin (ALB). These proteins have been identified in nonhominin palaeoproteomes as well and are consistently incorporated into the mineralized bone matrix (25,26).…”

Biologically and diagenetically derived peptide modifications in moa collagens

“…While others have reported several biologically and diagenetically derived PTMs [11,13], we identified four biological PTMs (table 2) out of five total modifications for the first time from fossil remains. We also detected three or potentially four novel diagenetic PTMs (table 2) that have not been previously detected from fossils.…”